There's an excellent book called CYCLING JAPAN, A Personal Guide to Exploring Japan by Bicycle, edited by Bryan Harrell, published by Kodansha, ISBN 4-7700-1742-1.
Amazon.com lists one new and one used in stock.
This is one complete cycling guide! It has lots of routes, each with a bilingual map, and detailed route descriptions, and it has plenty of routes for rides in an around Tokyo, and the surrounding Kanto region. The only thing is that it was published in 1993, so there may have been some changes to roads outlined in these routes.