Things to do in Boston

If you stay downtown the Freedom Trail hits a bunch of historical sights, Old North Church, Ironsides, Bunker Hill, etc. Boston rightly gets called the most-walkable US city.

The public transportation (subway) is easy and good. You can take it to and from Logan Airport in addition to lots of places around town.

Bell in Hand Tavern and eat Italian food in the North End. Cool city.

Have fun.

the aquarium is very cool - you can pack in a good solid 2 to 3 hours, see everything and really feel like you got your money's worth

Highly recommend Harpoon Brewery - regardless of how much you like their beer, their brewpub/bar/gift shop visitor area is top notch. I'll go there just to hang out, tour, no tour

Sam Adams is ok, nothing great

I have yet to check out all the museums , although I hear they are pretty good - I can say the science museum is shite, dont waste your time

To get lay of city, do the duck tour.
I know it's cheesy but it's a great way to get your bearings in that city.

Go to top of Prudential Center.
For Fenway, do the batting practice tour on game days only - get tickets in the morning for that day and you meet before game and get to go on field in stands and on green monster for batting practice, almost as good as the game itself. Tickets have been a little easier to get compared to the World Series years.
Definitely Mike's Pastry in Italian North End along with a meal just about anywhere.
Ye Olde Union Oyster House
Aquarium was just ok

If you have time for day trips, hit Newport Rhode Island and Maine coast is not that far away from airport.

I would say Cape Cod but it is going to be very crowded in July.