I think skiptons is the only real LFS in boston. Lovely Pets is in quincy, and is a decent sized place, but prices are high, and quality really isnt, IMO.
The place in everett is probably the other Sea Creatures.
But yeah, basically all the best shops are outside the city. Tropic Isle (framingham)has a great selection of fish and dry good, but their prices on fish are about 20% higher than everyone else, and their dry goods prices are just plain silly. ($149.99 for a mag7).
South of the city, Coral Reef Aquarium is Seekonk is great, with a good amount of aquacultured frags, great people, and their own line of equipment: "Skim-mate" skimmers, basically ER knockoffs, really nice, run like $200, their own line of Ca reactors, etc. Jeremy is a little quiet, but is great if you actually take the time to talk to him.
If your into Cichlids, Uncle Ned's Fish Factory is one of the best in the country (millis,ma?)
West of the city theres Beacon Aquarium in worcester, theyre pretty good, but I've only been there a couple times. Talk to Lourdes.
North theres Aquarium Gallery, and Aqua Addicts. Mike at AA imports a lot of his own stuff, IE decent refractometers for $40, large line of RO prefilters for like $4 each, etc, and generally has great prices on things. Salifert Mag kits are like $20, theyre 25+ everywhere else.
THeres plenty of good shops around, just look at 45 minute rides for most of them, becaues Skiptons closes at 6:30....and its tough to get into the center of Boston around that time.
bdelaney, did you go to BCHigh?