Dawes-Man made some good suggestions in a PM he sent me when I went to Tokyo in April:
A quick train ride from Akasaka… 5 minutes or so… will take you to a large modern cycle shop called Narashima Furendo and a very expensive, tiny, 1980s Italian boutique shop called Hip Hip Shake, which has a lot of nice frames - De Rosa, Colnago, Cinelli etc. and a lot of Campagnolo parts on display.
For classic Japanese touring parts there is
Hasegawa Shoukai, a 30 minute train ride from Akasaka station.