Hi there! I have relatives in Japan and i've been there a couple of times!
There are guitar shops EVERYWHERE, shibuya, shinjuku etc but THE PLACE to go to in Tokyo for guitars is Ochanomizu, its a few stops away from Shinjuku via the "Chuo Sen" (Central Line) in the JR Railways network.
This place is guitar heaven for us all. Imagine, orchard road, but every single shop selling guitars!!! I bought several guitars there already, they have new instruments, japanese brands, weird and out of this world accessories (things that make your guitar SMELL GOOD!?) and 2nd hand vintage instruments. I suggest you take a walk there!
The good thing is, customer is KING there. So try all the guitars you want, you can walk out empty handed after trying and they'll still bow down and kiss the ground etc.
I tried PRSes, Gibson and Fender Custom Shops, Tom Andersons, John Suhrs, Tylers, vintage yada yada... everything expensive. Have fun! if you need more directions PM me.