I'm in Boston. I'd suggest joining
Boston Reefers, the local reefing club. Most of my coral and live rock came from other reefers in the group (they have a good marketplace and often things area available for free/cheap). My tank itself actually came from another member of the group.
For stores, I go to European Aquatics in Malden. They keep good, healthy fish and get orders in weekly. Their coral is pretty decent too. They have a "live rock" tank that's it's own system (not on the same large system as all of the displays) where they've seeded dry rock and let it run. It's the best of both worlds if you're just getting started as there's zero risk of nasty pests and you get a jump start on bacteria and algae growth.
Love The Reef in Wilmington is great for coral. Their in-store selection is better than what you see online. They've got really good stuff.
Also for coral, check out Acro Garden in Concord. You can get more info on the Boston Reefer's page, but it's appointment only and run out of a guy's basement. He's been doing it for years and his setup is incredible... like could be a public aquarium incredible. He's got everything from the most basic of softies to the healthiest SPS you'll find. Absolutely worth it.
While I've never been personally, some people (who know what they're talking about) swear by Jay's aquatics in Salem, New Hampshire for fish and coral.
But again, I'd highly recommend joining Boston Reefers. It'll save you a lot of money in good quality coral in the long run. Yesterday I grabbed a 9 head candy cane frag (with some random Zoas on the stalk) and a 3 head (with 3 more growing) frag of Darth Maul zoas from a nearby reefer via the club for $15 total. Probably would have been $70+ at any store.
