Two places seem to get the most mention when this comes up
MinutemanNormandy FarmsBoth are close to commuter rail lines that go into Boston.
The historic walking tour, the Freedom Trail (known locally as "the stupid red line") visits several historical sites around the city. You really want decent weather for this and would be tiring for kids.
The Prudential tower has an observation deck that's great on a good day.
And then there's the
Duck Boat Tour in WWII amphib vehicle that rolls through parts of downtown Boston and ends up in the Charles River.
Lots to do, just don't even think about taking the HR into the city.