Tokyo

Shinjuku area

Shibuya area

Ikebukuro area

Tokyo-station area

Jimbo-cho<-the biggest bookstore area in Asia.

Other Area of Tokyo

Tokyo Bookstore Chains

Junkudo

http://www.junkudo.co.jp/mj/store/store_search.php

Kumazawa

http://www.kumabook.net

Keibundo bookstores

http://www.keibundo.co.jp/shop/index.html

LIBRO

http://www.libro.jp/shop/

Toranoana

http://www.toranoana.jp/shop/