I'm just going to do a quick plug: the guys at the Kichijoji branch of
Cycle Work Station know their gear, can fix damned near anything, and are honest and helpful almost to a fault.
I've dropped a lot of cash at
Y's Bike Academy in Akasaka-mitsuke over the years. I don't really trust them, as they cater to the non-Japanese-speaking financial crowd -- folks that have a lot of cash, don't really know their gear, but want to look good while they're riding their
Antares road bike around town. I used them to upgrade my
Hardrock XC from
Alivio drive-train and vee-brake setup to an all-
XTR disc-brake configuration. They really screwed up the install by putting the rear brake caliper on the front fork mount (and vice-versa) and fitting undersized rotors. I wasn't happy, especially as I had to swap out the stock forks for a Fox Vanilla to permit the installation of the wrong damned brake caliper. The guy that figured out what the Y's guy had done to my bike was surprised, and not a little bit irate, that they'd made such a fundamental mistake.
Then I found CWS while wandering around Kichijoji. They're just a little hole-in-the-wall shop, with various sorts of bicycles stacked all along the walls ... and a really decent selection of racing bike parts towards the back.
The clincher for me happened yesterday. The rear derailleur on the Hardrock somehow managed to get badly bent, so it kept trying to shift gears on its own. I took it to the Bridgestone dealer around the corner from the house, who took one look at it and declared it broken beyond repair. I figured that he'd never seen XTR gear before, so I took it over to CWS.
One of the kids there looked it over for about five minutes, then told me that they'd have it fixed by two that afternoon. Sure enough, when I returned, they'd not only straightened the derailleur bracket, but had also dialed in both shifters and replaced the chain. During the conversation, the kid ("Taku") asked if it was okay to speak English ... and it turns out that he was born and raised in NYC. I find that it's easier to talk about bike tech in English than Japanese, so we switched over to English and chatted about the repairs, the oddness of putting XTR onto a Hardrock, and the injuries that mandated that upgrade.
To sum up: if you're in west Tokyo with a busted bike, take it to Kichijoji CWS at 武蔵野市吉祥寺本町1-11-19 1F (042-2228-7787). They're competent and honest. When I build my racing bike, I'm going to use them for advice and parts sourcing.