Most of the shops are concentrated in Shinjuku! Though deals are what they used to be, theyre cheaper than online prices by at least 10%. Also buy fuji 100 and slide film while youre there
As a regular traveler to Japan these 20 years and have been to most of these stores in Tokyo I can only recommend two: MapCamera in Shinjuku and Fujiya in Nakano. I only shop for used Leica gear in Japan. This is because what I buy tend to be old and Japanese people tend to maintain their stuff much better. Also these two shops are beyond honest and will disclose any defects obvious or not. For other gear including Nikon etc, Hasselblad and Rolleiflex I buy online from US dealers. These things tend to be priced higher in Japan while Leica is competitive. I don’t know why. It might be the sheer volume of used gear available in the US.