Guitar Shogun

Most of the guitar shops in Tokyo are concentrated in 4 areas: Ochanomizu, Shibuya, Shinjuku, and Ikebukuro. Below is a non-exhaustive list of the

Big National Chains

Ishibashi

One of the biggest national chains with nearly two dozen shops (not all guitar-related) across Japan. They currently run 8 guitar shops in the Tokyo area. Shibuya, Shinjuku, and Ikebukuro each have a massive store, while there are 5 small specialty shops close together in Ochanomizu. The store is Shibuya is quite possibly the best guitar shop in the world. The amount of inventory is massive and it's over 60% high-end. I have heard that that store moves the largest amount of Gibson Custom product. 

Yamano

One of the oldest and largest all-around music chains in Japan with 45 stores nationwide.

Shimakura