Another +1 for Fenway and the Freedom Trail - the latter is delineated by red bricks laid in the middle of the concrete pavement (or sidewalk)!
As has been said the Cheers bar is an attraction, and you can also do a DUKW tour of the harbour with a recreation of the original "Tea Party". :lol:
Quincy Market is worth a tour as well - especially when it has pubs like the Black Rose complete with draught Guinness!
The pier area has some great seafood restaurants - lobster dinner overlooking the sea is a great evening! The oysters are fantastic too!
Subject to budget, the Boston Marriott Long Wharf is a great place to stay - right on the Harbour!
If you have a rental you could cruise Southwards on the East Coast to Plymouth (they have a replica of the Golden Hind, because that is where it is believed to have landed)!
Then a bit further South there is Cape Cod, with Martha's Vineyard (home of the Kennedy family) a ferry ride away from Falmouth(assuming it is running)!
Had some great weekends in Boston when I worked for a US domiciled insurance company and had to attend training courses in MA!