Within Boston, I'd recommend the JFK museum, the historic walk around the centre of the city near Fanuiel Hall and try and go and see a Red Sox game, Fenway park is the oldest and probably most atmospheric baseball ground in the US, and I personally always think it is great to see people at play to get a feel for what a country is like. There are also good whale-watching trips out from Boston as well.
Cape Cod is gorgeous, you could drive down to Plymouth and up the Cape, or get a ferry over to Provincetown from Boston