We took a guided tour for first half (boston common to Faniell Hall. Then ate lunch (family of 4), then continued on our own up through North End Church, then caught T back to hotel (stayed near Copley Square.) Next morning we took subway to community college exit and walked over to Bunker Hill (end of Freedom Trail) (nice Dunkin Donuts between T and Bunker Hill.) Arrived shortly after 9:00 a.m. before the crowds (in the summer later in the day they have to give out timed tickets to climb the stairs within the monument at Bunker Hill.) We toured Bunker Hill and the USS Consititution and museum (again before the crowds hit), ate lunch in the North End, and were at the Harbor for our sightseeing cruise by 2:30.
If you have 2 days to do it, this seemed to work so much better than trying to accomplish it all in one day. While not too taxing physically, it's alot of history/information to cram into one day.