There is a Lonely Planet Tokyo and Kyoto. IMO, the Lonely Planet series is the best, I used LP Japan extensively while I was there. (
Amazon.com: lonely planet japan )
I also used the Japan Handbook by J. D. Bisignani. (
Amazon.com: Japan Handbook (Moon Handbooks : Japan): J. D. Bisignani: Books ) It has a different focus from the Lonely Planet books... far less practical in terms of getting around, but more cultural info, festivals, places to visit that are off the beaten path, etc.