We loved Boston!
Hammersley's Bistro is a good choice if you are not seafood fans. We ate italian food at Strega in the North End...I know there are countless options. The Freedom Trail is wonderful, as are the other sights mentioned above. Taxis are inexpensive and easy to come by.
Enjoy your trip!

Personally, I found the New England Holocaust Memorial to be fascinating. http://www.nehm.com/

I recommend going at night, when it is even more poignant and beautiful. It is right next to some touristy/historic restaurants. Including the oldest restaurant in the United States that boasts being a former hang out for several revolutionaries. (sadly, i can't recall the name of it right now.)

erinannie, Union Oyster House is across the street.

That monument/ art gives me pauce everytime I see it. In the heat of the summer when the gases release, on a cold wintry day as the gas billows like steam....it is such a powerful piece and memorial, and reminder.

Neptune Oyster is for my taste the best place for seafood in the close-in Boston area. Will agree with amyb about the seafood spots in Essex and environs. Not at all a fan of Union Oyster House -- like Neptune Oyster much better.