The International Schools Directory is an extensive listing of International Schools in Japan including preschools & kindergartens, elementary schools, junior & senior high schools, other foreign language schools, and Japanese schools for returnees.
The Education in Japan Community Blog is an invaluable site covering many different topics related to educating your child in Japan. With articles such as the Guide to Surviving Yochien (Kindergarten) in Japan and numerous directories of local schools, both Japanese and international, plus an extensive list of resource links, this site is for anyone with preschool or school aged children in Japan.
The Guide to International Schools in Japan by Caroline Pover features many of the international schools in Japan where they answer questions commonly asked by parents looking for a school for their child. The book can help you create a shortlist of schools after which you should at least contact and possibly visit each school yourself before making any decisions.