This site has a lot of second hand camera gears list from many shop all over Japan and it is always up to date.
Japanese language only but you should be able to use
live translation feature from
google translation app on your phone (never go to japan without this app!) to help read the site.
I already sat the filter to point at Pentax.
When you click to view product details, scroll down to see address or map of the saler's store. Fujiya and MapCamera list their gears on this website too. You can order online if you can work with Japanese language. I often check for the best price here first then find out if the store is in Tokyo where I can go and hand on test it.
MapCamera has their own web site as
rojaba put the link up on the very first post. I think MapCamera web site is pretty good and their price is quit competitive too. Map to their store in Shinjuku is
here. It is very close to PentaxSquare, and Tokyo Goverment Office Building which you can go up to the top floor for 360 view of tokyo for free, and it is shinjuku, needless to say everyone go there. And a Map to Fujiya near Nakano station is
here. If you like night stree photography, Nakano at night is good. I can not say it is better than Shinjuku but if you already go there, wait until night time and you will get a lot of nice street light photo from there.
I believe both store offer tax free to tourist if you show them your passport.