Other things to see in and near :
(1) the bar "Cheers", which was used as the basis for a famous TV show (although the show was actually filmed in LA, the bar is real and is still in Boston, and has lots of information about the show),
(2) Fenway Park, the oldest US baseball park in the country (opened in 1912) and still used daily for Boston Red Sox games (when they are in town),
(3) Bunker Hill--site of one of the first battles of the Revolutionary War
(4) all of the well-known colleges in Boston--Harvard, MIT, Boston College, Boston University, Bentley, Northeastern, Brandeis, University of Massachusetts at Boston, etc. There are actually 52 colleges in the Boston area--the most in any metropolitan area in the country. The city of Cambridge, just outside of Harvard, is especially nice.
(5) Salem, a short distance away--is famous for its "witch" trials back in 1692-1693. There is a Salem Witch Museum, many exhibits, and supposedly haunted home.
Also, I would take the ferry from downtown Boston (near Faneuil Hall) over to the US Constitution and Bunker Hill. The price is cheap and it will save you a ton of walking.
P.S. I have been in Boston three times.