Three books on Japanese cinema I've found interesting are:
The Waves at Genji's Door by Joan Mellen. This is a good read, and it covers a lot of territory. I think the major weakness is that she tends to focus her discussion on the screenplay of the film almost exclusively. So far as I can tell, she hasn't much visual sense. Still, it's very valuable when it comes to thematic analysis and filling in important facts about the historical context of the film. (But if you have much knowledge of Japanese history, this may not be so valuable.)
Eros Plus Massacre by David Desser. This basically covers the Japanese New Wave, and what I've read of it has been excellent. Unfortunately, since a good many of the films discussed here are unavailable to me (or at least unavailable to me in subtitled prints), I haven't read much of it. I doubt I'd get much from those chapters discussing films I've not seen.
Japanese Films: A Filmography and Commentary, 1921-1989 by Beverley Bare Buehrer. This isn't so valuable as a work of criticism, but it might help structure your viewing. The book covers a list of about seventy-five of the most historically important and critically acclaimed Japanese films. There's a short plot synopsis of each movie and a page or two or critical discussion.
Also, there's an interesting article on Mizoguchi's Ugetsu and Sansho the Bailiff in Robin Wood's Personal Views.