The kids loves the Duck Tour as they each get a chance to steer the boat. Great photo op. The Children's Museum would be fun. I think the Science museum might be too mature for them (though it is geared towards kids). I normally wouldn't recommend it, but they'd probably like the street performers that frequent the area around Faneuil Hall. Freedom Trail could be nice.
Helpful Link: http://www.nineblue.com/kids/attract...px?city=Boston