these guys make NJS frames and their shop's in tokyo.
not in central but not that far out either.

http://www2u.biglobe.ne.jp/~cherubim/

Also, check these places,
they're not in tokyo, but next pref.

http://www.cycleland.jp/
http://www.cycle-recycle-depot.com/

I haven't been to any, but I would visit if i were in Japan.
maybe next time.