I can recommend this series by John Hall which I read when I first started studying Japanese history.

Hall, John Whitney et al. The Cambridge history of Japan. Cambridge: Cambridge University Press.

1993 Volume I. Ancient Japan.

1995 Volume II. Heian Japan.

1999 Volume III. Medieval Japan.

1994 Volume IV. Early modern Japan.

1993 Volume V. The nineteenth century.

1991 Volume VI. The twentieth century.

Here is also a book that gives you a broad overview:

Totman, Conrad 2000 A history of Japan. Malden, Mass. and Oxford: Blackwell

I also enjoyed this book about modern Japan:

Jansen, Marius B. 2000 The making of modern Japan. Cambridge, Mass: Belknap Press of Harvard Univ. Press

You could also check out this bibliography at Cambridge University:

Peter Kornicki, Cambridge Univ: “Bibliography of Japanese History up to 1912” http://intranet.ames.cam.ac.uk/jbib/

Be aware that all of these are scientific. If you want I can also recommend a few books that might be easier to digest.

For the first Japanese encounters with the West, Masao Miyoshi's As We Saw Them: The First Japanese Embassy to the United States details the first Shogunal embassy to the US. W. G. Beasley's Japan Encounters the Barbarian: Japanese Travellers in America and Europe also covers the same topic, albeit more comprehensively. Beasley also wrote an excellent introductory history to Japan, The Japanese Experience: A Short History of Japan, which is worth looking into if the Cambridge histories of the Jansen texts are too intimidating. Tuttle has recently combined Edward Seidensticker's two-volume history of Tokyo into a single edition, Tokyo from Edo to Showa 1867-1989.