I would say the top two in terms of overall "wow!" and reputation are Landry's (the friendliest by far) and Wheelworks (an institution, founded by Olympic cyclist John Allis and just amazing in terms of selection). Wheelworks has three branches - Ace is in Porter Square (Cambridge/Somerville line) and given its location gets a lot of commuter business; Belmont Wheelworks is a bit more suburban and has more of a road focus; Wheelworks Too is next door and has secondhand and kid bikes. I find the service at Wheelworks (all) can be hit or miss; there are fantastic people and the occasional clunker.
If I was going to purchase a mountain bike (or BMX for that matter), I'd go over to JRA in Medford. Fantastic guys there and they are nuts for dirt. They'll sell you anything, but they really like being offroad. Owner and his wife are big into cross too. The atmosphere there reminds me of record stores in the 80s - lots of staff who love it so much that you figure they'd be hanging around even if not paid. (and case this isn't clear, it's a compliment!)