I started private Japanese lessons recently and my teacher introduced me to this very cool store, Bonjinsha. They are a book store that carries nothing but books for learning Japanese (and for teaching it). They have a ton of books. Probaby 5 or 6 times as many as like Book 1st or Kinokuniya. There are 2 stores, one in Tokyo and one in Osaka. If you are looking for books for studying it would be a good place to check out. The one in Tokyo is near the Nagatacho station (永田町駅) which is also connected to the Akasaka−Mitsuke station (赤坂見附), that's 5 lines to choose from. Marunouchi, Ginza, Hanzomon, Yurakucho and Nanboku lines.