I'm not a historian, but the following books range from essential to important or interesting (there are of course many, many more):

Tokugawa:

• Toby - State And Diplomacy In Early Modern Japan: Asia In The Development Of The Tokugawa Bakufu

• Totman - Politics in the Tokugawa Bakufu, 1600-1843

• Nakane - Tokugawa Japan: The Social and Economic Antecedents of Modern Japan

• Ooms - Tokugawa Ideology: Early Constructs, 1570-1680

• Scheiner - Japanese Thought in the Tokugawa Period, 1600-1868: Methods and Metaphors

• Bellah - Tokugawa Religion

• Najita - Readings in Tokugawa Thought

• Harootunian - Things Seen and Unseen: Discourse and Ideology in Tokugawa Nativism

• Harootunian - Toward Restoration: The Growth of Political Consciousness in Tokugawa, Japan

• Totman - The Collapse of the Tokugawa Bakufu, 1862-1868

Meiji:

• Mounsey - The Satsuma Rebellion: An Episode of Modern Japanese History

• Jansen - The Emergence of Meiji Japan

• Jansen - The Making of Modern Japan

• Jansen - Sakamoto Ryoma and the Meiji Restoration

• Beasley - The Meiji Restoration

• Craig - Choshu in the Meiji Restoration

• Wilson - Patriots and Redeemers in Japan: Motives in the Meiji Restoration

• Hane - Peasants, Rebels, Women, and Outcastes: The Underside of Modern Japan

• Ketelaar - Of Heretics and Martyrs in Meiji Japan

• Irokawa - The Culture of the Meiji Period

• Gluck - Japan's Modern Myths: Ideology in the Late Meiji Period

If you're interested in these two periods, try to read the table of contents of each book (available on Amazon, Google Books, or easily found via Google otherwise), coupled with reviews (Amazon, Jstor, and so on), and you're likely going to find something you want to delve into, and that can be a way to find other quality books too, by other authors, on the same periods.