Despite the belief in some circles that information on the Edo and Bakumatsu periods is scarce, there is actually a wealth of information to be found, in Japanese, English, French, and German, among other languages. I will attempt to list texts below. Some of these I have used, some I have not...but all of them are out there. Worldcat has been a great help in locating books. Where possible, I will include comments on works which I have made use of. Citations are in the Chicago format. Names, of course, are given in the Japanese order- family name first, then given name. Also, please note that because of issues with HTML I have been unable to incorporate macrons.
I admit I am not perfect- if I have made an error, please let me know.
*Akizuki Teijiro. Iken Iko. Okayamashi : Akizuki Kazutsugu, 1913.
*Arai Ikunosuke. Wa-Ei Taiyaku Jisho. Tokyo: Kobayashi Shinbe, 1872.
Early Japanese-English dictionary compiled by Tokugawa navy officer Arai Ikunosuke.
*Hayashi Gonsuke. Waga Shichijuunen wo Kataru. Tokyo: Daiichi Shobo, 1936.
Autobiographical work by Hayashi Gonsuke, the grandson of his namesake Hayashi Gonsuke, who was a senior Aizu military commander who fought at the Battle of Toba-Fushimi and died of his wounds. A reprint was published by Yumani Shobo in 2002.
*Hayashi Isao. Kazusa no Kuni Jozai-hanshu ichimonji daimyo Hayashi-koke kankei shiryoshu. Chiba-ken Kisarazu-shi : Hayashi Eiichi, 1988.
*Hayashi Tadataka. Ichimu Hayashi o Shuko Boshin Shutsujin-ki Tokyo: n.p., n.d.
Text authored by Hayashi Tadataka, the former daimyo of Jozai, recording his experiences during the period of the Boshin War.
*Kada Kuninori. Kuwana-han Kyoto Shoshidai chu no jijo. Tokyo: Tokyo Ishin Shiryo Hensankai: 1917.
*Katsu Kaishu. Hikawa Seiwa. edited by Eto Jun and Matsumura Rei. Tokyo: Kodansha Gakujutsu-bunko, 2005.
This work is very useful because Katsu Kaishu, a longtime veteran of both the Shogunate and the Meiji government, talks about a variety of things in his life experience, as well as the wide range of people who he has encountered. For instance, he discusses the foundation of Japan's modern navy-- and notes that it was the Shogunate which laid its foundations. However, precisely because of the aforementioned wide purview of this work, sometimes this text feels like it's rambling, and so it takes some patience to properly utilize.
*Kawai Tsugunosuke. Chiritsubo: Kawai Tsugunosuke Nikki. edited by Ando Hideo. Tokyo: Heibonsha, 1974.
The diary of Nagaoka domain senior councilor Kawai Tsugunosuke, who had a history of scholar connections to Yamamoto Kakuma of Aizu, Yoshida Shoin of Choshu, Sakuma Shozan of Matsushiro, as well as Katsu Kaishu. Kawai, renowned for his purchase and use of high-tech weapons such as Gatling guns, fought in the Boshin War, and was wounded in action during the defense of Nagaoka. He escaped to Aizu, and in the words of historian Harold Bolitho, died a "slow, agonizing" death there from gangrene. In this journal he makes many references to the activities of Aizu and other domains in the late 1860s.
*Kitahara Masanaga. Shichinenshi 2 vols. Tokyo: Tokyo Daigaku Shuppankai, 1978. (republication of 1904 version)
Exhaustive compilation of primary documents pertaining to the Aizu domain and its role in the politics and affairs of the 1860s. A man of Aizu extraction himself, Kitahara was the brother-in-law of Jinbo Yukiko, a member of the famous fighting women's unit, the Aizu-Joshitai.
*Kuwana-han Shiryo Shusei. Kuwana: Kuwana-shi Kyoiku Iinkai, 1990.
A compilation of historical resources pertaining to the Kuwana domain.
*Maeda Nariyasu. Sarugaku menhai ron. Tokyo: Ishiguro Bunkichi, 1934.
*Matsudaira Kataharu. Hoshina Masayuki Gazo. Tokyo: Tokyo Teikoku Daigaku, 1909.
*Matsudaira Tsuneo. Honpohin no shinshutsu ni kansuru Eikoku-gawa yoron. Tokyo: n.p., 1934.
*Matsumoto Ryojun. Yojoho. n.p.: n.p., 1864.
*van Meerdervoort, JLC Pompe, Matsumoto Ryojun, and Ogata Koan. Korera chijun. Osaka: Akitaya Tauemon, 1857.
*Nagakura Shinpachi. Shinsengumi Tenmatsu-ki. Tokyo: Shin Jinbutsu Oraisha, 2003.
Another memoir written in the same era as Katsu Kaishu's work. The author of Shinsengumi Tenmatsu-ki was Nagakura Shinpachi, a man who served in the highly controversial Kyoto police unit known as Shinsengumi. Nagakura, having been born into the society of Edo-based retainers of the various domains (his father served the daimyo of Matsumae), and having been trained as a swordsman, was acquainted with many figures who later became important in the history of the Bakumatsu era.
*Niijima Yaeko. Niijima Yae Yuigon. Kyoto: Doshisha, 1932.
The last will of Niijima (Yamamoto) Yaeko, the sister of Yamamoto Kakuma, who fought in the Battle of Aizu as an artillery commander and raider.
*Numa Morikazu. Numa Morikazu Kodanshu. Tokyo: Iwasaki Yoshimasa, 1882.
*Ogasawara Naganari. Ogasawara Naganari Zenshu. Tokyo: Heibonsha, 1936.
*Otori Keisuke. Bakumatsu Jissenshi. Tokyo: Tokyo Daigaku Shuppankai, 1981.
Reprint of the 1911 and 1969 editions; this book, written by Otori Keisuke, discusses the events of the Boshin War from his perspective.
*Shiba Goro. Remembering Aizu: The Testament of Shiba Goro. edited by Ishimitsu Mahito, trans. by Teruko Craig. Honolulu: University of Hawai'i Press, 1999.
Memoir written by the Aizu native Shiba Goro, who was a child at the time of the Boshin War and lived through the destruction of Aizu. Useful for acquiring a better understanding of the human cost of the war, it also provides the reader with a perspective on the events surrounding the reorganization of the country from a coalition of domains into a single unified body under the Meiji government. For the original Japanese, see: Shiba Goro. Aru Meijijin no Kiroku : Aizujin Shiba Goro no Isho. edited by Ishimitsu Mahito. Tokyo: Chuo-koronsha, 1971.
*Shibukawa Sukedayu. Nisshinroku : Sendai-han ishinshi shinkiroku. Sendai: Hobundo, 1983.
*Takagi Morinosuke. Numasawa Michiko-kun no Den. Tokyo: Numazawa Shichiro, 1913.
Biography of Numasawa Michiko, one of the key matriarchs of the mid-to-upper Aizu samurai families. Includes extensive information on her son, Shichiro, who published the work. At the end is appended Sei'un-ki, a memoir by former senior Aizu retainer Saigo Tanomo. Not only is this work indispensable to those who wish to acquire a better understanding of the human picture of Aizu's involvement in the Boshin War, I believe it is also indispensable for people interested in the Shinsengumi, as Numasawa Shichiro's adopted son was the 3rd son of Shinsengumi captain Saitou Hajime (also known as Fujita Goro or Yamaguchi Jiro).
*Takahashi Bonsen. Ashigaru Kikigaki. Tokyo: Kaimei Shoin, 1977.
Covers the lifestyle and customs of the ashigaru of the Sendai domain.
*Takamatsu Ryoun. Takamatsu Ryoun-o keirekidan. Hakodate Senso Shiryo. Tokyo: Tokyo Daigaku Shuppankai, 1979.
This book is useful for those who are interested in the Boshin War, Enomoto Takeaki, or even the circumstances surrounding the last days of Hijikata Toshizo. However, it offers a source of information on an aspect of the Bakumatsu and Boshin War not often covered: that of medicine. The author, a brother of the Shogunal Army field commander Furuya Sakuzaemon, was trained in Western (French and English) medical techniques, and opened up the first Red Cross hospital in Japan, in Hakodate, just before the battle there.
*Watanabe Katsunosuke. Bakumatsu tenkinden : Kuwana-han kanjonin Watanabe Katsunosuke no nikki. edited by Honma Kanji. Nagoya: Efue Shuppan, 1988.
*Yamakawa Hiroshi. Kyoto Shugoshoku Shimatsu. 2 vols. Tokyo: Heibonsha, 1966
A crucial text which chronicles the history of the Kyoto Shugoshoku (Kyoto Protector's Office), which the Aizu lord Matsudaira Katamori held during the 1860s. The author of the text, Yamakawa Hiroshi, was the brother of Yamakawa Kenjiro (whose work appears below), and was a senior retainer of Aizu prior to the fall of the domain. In the Meiji era, he became a military officer and an educator, and was part of the "Aizu network" in which his brother was a focal point.
*Yamakawa Kenjiro. Aizu Boshin Senshi. Tokyo: Tokyo Daigaku Shuppankai, 1931.
This book is in a class of its own. It is of monumental length (741 pages!), written and compiled by Yamakawa Kenjiro, a former Aizu samurai who was important as president of Tokyo University in the Meiji period. Furthermore, he oversaw the affairs of his former lord, Matsudaira Katamori, and came from a family that was part of the vast network of former Aizu retainers who tried to stick together in the Meiji era. The text itself goes through the entire history of Aizu in the Boshin War, from the eve of the Battle of Toba-Fushimi all the way to the defeat, surrender, and subsequent exile of Aizu's samurai population. He also includes information on Aizu's administrative structure and holdings, and even provides maps of the domain and the castle town. All told, an invariable resource on Aizu, and on the war.
*Yamamoto Kakuma. Yamamoto Kakuma Kenpaku. n.p.:n.p, 1868.
A petition dictated by the blinded Aizu retainer Yamamoto Kakuma on national reform, during the time that he was a prisoner of war in the custody of the Satsuma domain. Rather notably, Kakuma makes use of the term bunmei (enlightenment), several years before Fukuzawa Yukichi, the famed proponent of that term.
*Abe Muneo. Sendai-han Date-ke no Onnatachi. Sendai: Hobundo, 1987.
*Adachi Yoshio. Aizu Tsuruga-jo no Onnatachi. Aizu-Wakamatsu: Rekishi Shunjusha, 1981.
*Asamori Kaname. Bakumatsu no Kakuro Itakura Katsukiyo. Tokyo: Fukutake Shoten, 1975.
*Asano Gengo. Sendai-han Shi. Tokyo: Toyo shoin, 1976.
*Asano Gengo. Yonezawa-han Shi. Tokyo: Toyo Shoin, 1975.
*Drixler, Fabian Franz. Infanticide and its enemies : demography and discursive change in Sendai at the turn of the nineteenth century. Cambridge: Harvard University, 2004.
*Fukumoto Ryu. Ware toshisezu: Meiji wo Ikita Otori Keisuke. Tokyo: Kokusho-kankokai, 2004.
*Fukumoto Takehisa. Aizu Onna Senki. Tokyo: Chikuma Shobo, 1983.
Though this book is fiction, it represents a part of the Boshin War which has received next to no coverage in Western scholarship: that of women. Can offer good peripheral reading for a scholar covering the topic.
*Fukumoto Takehisa. Niijima Jo to sono tsuma. Tokyo: Shinchosha, 1983.
Covers the history of Niijima Jo, the Meiji-era evangelist, and his wife Yamamoto Yae, who was the daughter of an Aizu samurai, and who fought in the Boshin War.
*Fukunaga Kyosuke. Kaisho Arai Ikunosuke. Tokyo: Morikita Shoten, 1943.
Covers the life of Arai Ikunosuke, Navy Minister of the Ezo Republic in 1869.
*Harada Akira. Arai Ikunosuke. Tokyo: Yoshikawa Kobunkan, 1994.
*Hirao Nobuko. Kurofune Zenya no Deai: Hogei Sencho Kuupaa no Raiko. Tokyo: Nihon Hosso Shuppan Kyokai, 1994.
Presents the history behind one of the untold stories of early Japanese-American interaction: that of the whaling ship Manhattan, commanded by one Captain Cooper, and its arrival off the coast of Japan. Vital for anyone studying the historical background to the Shogunate's awareness of the Americans prior to Perry.
*Hoshi Ryoichi. Aizu Shogun Yamakawa Hiroshi. Tokyo: Shin Jinbutsu Oraisha, 1994.
*Hoshi Ryoichi. Bakumatsu no Aizu-han: Unmei wo Kimeta Joraku. Tokyo: Chuko-shinsho, 2001.
Scholarly text covering various aspects of the Aizu domain's history during the Bakumatsu period. Presents new and fascinating information to light, such as Aizu's efforts at implementing Western-style mining techniques to improve its wealth, or the chronic illness of the Aizu lord, Matsudaira Katamori.
*Hoshi Ryoichi. Sendai Boshin senshi : hoppo seiken wo mezashita yushatachi. Tokyo: Sanshusha, 2005
An excellent book about the Boshin War from the perspective of the north-- this time focusing on the Sendai domain. Sendai was the largest domain in the north by sheer income rating (625,000 koku to Aizu's 230,000), so to understand the course of the war in northern Japan, this book and others like it are essential, and it is my sincere hope that Western scholars take full advantage of this untapped resource.
*Hoshi Ryoichi. Yamakawa Kenjiro-den: Byakko taishi kara Teidai socho e. Tokyo: Heibonsha, 2003.
*Iechika Yoshiki. Komei Tenno to "Ikkaiso": Bakumatsu Ishin no Shinshiten. Tokyo: Bungei Shunju, 2002.
*Ishikawa Yasujiro. Numa Morikazu. Tokyo: Mainichi Shinbunsha, 1901.
Covers the life of Numa Morikazu, a senior officer in the Shogun's military who became a political and journalistic figure in the Meiji era, as well as an educator. Numa is notable for having taught some of the bright minds of the Meiji era, among them two men of Aizu extraction, Takamine Hideo (later a student of Fukuzawa Yukichi) and Shiba Shiro (also known by his pen name "Tokai Sanshi"; later a student at the University of Pennsylvania). A reprint of this text was released in 1993 by Ozorasha.
*Kaga Hanshu Maeda Nariyasu. Kanazawa : Ishikawa Kenritsu Rekishi Hakubutsukan, 1995.
*Kidono Teruo. Denki Nagai Genba-no-Kami Naoyuki. Okazaki-shi: Kidono Teruo, 1986.
*Koga Shiro. Otori Keisuke: Hijikata Toshizo to no Shukkai to Wakare. Tokyo: Sairyusha, 1993.
Discusses the interactions between Otori Keisuke and Hijikata Toshizo, the famed vice-commander of the Shinsengumi.
*Kori Yoshitake. Kuwana-han Boshin Senki. Tokyo: Shin Jinbutsu Oraisha, 2006.
*Kurokawa Ryu. Yamakawa Futaba-sensei. Tokyo: Oinkai, 1910.
*Matsudaira Katamori no Subete. Tokyo: Shin Jinbutsu Oraisha, 1984.
Exhaustive work about the life and actions of Matsudaira Katamori, the lord of Aizu. Includes his family life, his character traits, his politics, and his connections to other figures of the period, such as Tokugawa Yoshinobu, Matsudaira Shungaku, and Shimazu Hisamitsu, among others.
*Matsudaira Sadaaki no Subete. Tokyo: Shin Jinbutsu Oraisha, 1998.
*Mizusawa Shigeo. Nakano Takeko to Joshitai : Aizu Boshin Senso to Joshitaicho Nakano Takeko shiwa. Aizuwakamatsu-shi : Rekishi Shunju Shuppan, 2002.
*Nagasawa Kamio. Niijima Yaeko Kaisoroku. Tokyo: Ozorasha, 1996.
*Nakamura Akihiko. Dappan Daimyo no Boshin-Sensou: Kazusa-Jozai Hanshu Hayashi Tadataka no Shogai. Tokyo: Chuko-shinsho, 2000.
A text exploring the life and circumstances of Hayashi Tadataka (1848-1941), the only fudai daimyo to invoke his hereditary obligation of loyalty to the Tokugawa house, and go to war in the Boshin War.
*Noguchi Shin'ichi. Aizu-han. Tokyo: Gendai Shokan, 2005.
Covers the history of Aizu from 1600 through 1868. Admittedly a text intended for more of a general audience, it nonetheless contains vital information still unseen in Western scholarship on the Edo period.
*Obayashi Akio. Kyoto to Sendai-han: Tsuketari Osaka to Sendai-han. Sendai: Gararii Obayashi, 1995.
*Ogasawara Ikinokami Nagamichi. Tokyo: n.p., 1943.
*Oishi Manabu. Shinsengumi: "Saigo no Bushi" no Jitsuzo. Tokyo: Chuko-shinsho, 2004.
Innovative text which covers much unexplored terrain in dealing with the history of the controversial Shinsengumi. Discusses their history, their composition, and even such unexplored topics as their unit-wide training with firearms following the events of summer 1864.
*Onodera Eiko. Boshin Nanboku Senso to Tohoku Seiken. Sendai: Kita-no-sha hen, 2004.
Provides useful background on the Boshin War, in particular focusing on the oft-ignored story of the northern domains. Includes background on the Ouetsu Reppan Doumei (Northern Alliance) and the short-lived polity of Emperor Tobu.
*Ooms, Herman. Charismatic Bureaucrat: A Political Biography of Matsudaira Sadanobu, 1758-1829. Chicago: University of Chicago Press, 1975.
This book definitely gets my full recommendation. A thorough study of the life and actions of a largely misunderstood political figure, this text provides good background for the reasons and history behind the situation that Japan faced when entering the Bakumatsu period. Also has vital information on the famines of the late 18th century and how they affected the domains of the north, as well as those domains' efforts at assisting each other.
*Osaka Shingo. Arai Ikunosuke den : Hokkaido kyoiku no senkusha. Sapporo : Hokkai Taimususha, 1967.
*Sasaki Jo. Bakushintachi to gijutsu rikkoku. Tokyo: Shueisha, 2006.
*Sugihara Ken and Yanagihara Toyotaro. Numa-sensei no Den. Tokyo: Mainichi Shinbunsha, 1890.
*Suzuki Yoshio. Boshin no banka : Kuwana hanshi jonetsu no funsenroku. Tokyo: Shin Nihon Hoki Shuppankai, 1987.
*Takakura Jun. Sendai-han Keibatsu-ki. Sendai: Takakura Jun, 1988.
*Takano Kiyoshi. Tokugawa Yoshinobu: Kindai Nihon no Enshutsusha. Tokyo: Nihon Hosso Shuppan Kyokai, 1997.
Concise text analyzing the life, background and actions of Tokugawa Yoshinobu and those who surrounded him.
*Tokugawa Motoko. Tooi Uta: Tokugawa Hakushaku fujin no nanajuugonen. Tokyo: Bungei shunju, 2005.
*Tokugawa Munefusa. Saigo no Bakkaku: Tokugawa-ke ni tsutawaru yonjuunananin no shinjitsu. Tokyo: Kodansha, 2006.
*Tokugawa Munefusa. Tokugawa Yonbyakunen no Naisho-banashi. 2 vols. Tokyo: Bungei Shunju, 2004.
*Tokugawa Yoshitomo. Tokugawa Yoshinobu-ke ni yokoso : wagaya ni tsutawaru aisubeki "saigo no shogun" no yokogao. Tokyo: Shueisha, 1997.
*Tokugawa Yoshitomo. Tokugawa Yoshinobu-ke no shokutaku. Tokyo: Bungei Shunju, 2005.
*Tokunaga Shin'ichiro. Bakumatsu Kakuryoden. Tokyo: Mainichi Shinbunsha, 1982.
Text dealing with the senior councilors (roju) of the Tokugawa government during the Bakumatsu period.
*Totman, Conrad. The Collapse of the Tokugawa Bakufu: 1862-1868. Honolulu: University of Hawai'i Press, 1980.
Very important text for Anglophone scholars studying the Bakumatsu period. Analyzes the issues surrounding the Shogunate's fall from a variety of perspectives. All in all, a remarkably well-crafted book for a field of study that is still largely unexplored in English.
*Yokoyama Takaharu. Mie Bakumatsu Ishin senki: Todo-han, Kuwana-han no Boshin-senso. Osaka: Sogensha, 1999.
*Yoshimura Yasushi. Shingan no Hito Yamamoto Kakuma. Tokyo: Kobunsha, 1986.