In Boston, i'd rank the top 3 shops as follows

1.) Revolution - They sell track frames and parts, and sponsored an alleycat. They're a bit out of the way for me though.
2.) Boston Bikes - They have a nice selection of track parts and have a lot of experience with fixies. They're dumping BMX and are arranging to import Keirin frames.
3.) Broadway Bicycle School - IRO dealer. The wrench wenches (don't call them that) are really helpful, but they're not always the most knowledgeable. A great place to do work on your bike.

International Bicycle is an upscale roadie haven. Great selection, but higher than average prices. They refer to fixed gears exclusively as "that kind of bike." and have *no* experience working on them. On the upside, they're really nice and helpful.

I haven't been to Cambridge Bikes in quite some time, but the last time I was there, it took forever to get someone to help me, and they were kind of snotty.

Back Bay Bicycle was equally as underwhelming, though they do sell surly cross frames.