Boston bike shops
Bikes Not Bombs: Non-profit used-bike repair place. Everything is used and not hugely cheap for what you're getting but it's a great cause and I never feel bad spending money or volunteering there. The only downside is that they tend to sell a lot of older bike-boom era bikes with 27inch wheels. Check with them. Most components on the old bikes will be new and the bikes overhauled and solid, but not hugely high end. Prices are between $300-600.
Quad Bikes: Another non-profit. They sell refurbished bikes taken from Harvard Campus but are usually out of them. They order Surly bikes and some other stuff and are pretty cool if you're looking for something new.
Broadway Bicycle School: Mostly a repair shop and teaching center but they do sell some bikes to. Their new bikes are basically all what you are looking for but the selection is not huge. I think they might get their used bikes from BNB.
Open Bicycle: A new shop started this last year by bicycle-scene hipsters. It almost a entirely fixed gear shop. It looks like a boutique and they sell showcase lots of work by local framebuilders but also sell some reasonably priced (IIRC) "vintage" bikes that are basically what you are looking for. Their prices aren't any higher than what you'd find in other shops though.
Superb: They're opening up soon in Boston and looks like they're going to be pretty awesome and definitely like what you are looking for. Another sort of bike-scene shop, it seems. Not sure what they'll have for used stuff, yet.