I too have done all the fish stores north of the city. From where your at Skipton's would be my first pick. You need to go there during the day before 2pm or so or go later just before they close on weekdays. You really can't beat the knowledge base there with B, Anthony, and Ed.
AA is very good on prices and not nearly the zoo that can be Jay's. Pat has a lot of good fish and has been good about ordering specific fish I was looking for. His coral selection is not huge but representative. It is very close to Jay's as well so I usually do them at the same time. They also usually have the best prices on dry goods and stocks a lot of stuff from Bulk Reef Supply that the other don't as well as CPR stuff, Brightwell Aquatics supplements, and he has a good deal on boxes of Instant Ocean.
If you are willing to venture south Coral Reef Aquarium is a nice place for coral.
I am sorry to hear about Salt Water City as I went there just once after they moved and it looked they had a lot of space to grow into.
A small little shop to check out is Pets Plus up in Londonderry. Matt got me a great deal on my new tank and he has a small, well priced selection of fish. There is also one in Tewksbury but it has only like 3 or 4 tanks of salt.