Lots of great suggestions. I live in Boston, so let me add votes for

1) Aquarium. Touristy but fun
2) Museum of Science. DO NOT go without seeing the Omni theater - its awesome. Also, be sure to check out the lighting show. I bring everyone to the Omni theatre that is in town and they all love it
3) Duck tours, if you must May be chilly in April, dress right!
4) Don't miss downtown crossing, Newbury Street, The Boston Commons, Freedom Trail, Esplanade, and be SURE to get food in a real chinese place in Chinatown. These are all downtown and easy to do
5) going up the hancock tower and prudetial are good. if you want a nice dinner with a view, go to Top of the Hub at the top of the Pru. Very nice and lunch is not that costly
6) Day trip up to Salem MA or Gloucester, MA is good if you like ocean-y stuff.
7) See the Constitution, near the North End
8) Wang Ctr and Museum of Fine Arts are good. There are lots of eclectic museums in/around Boston that are great to check out.