the frog pond is a ton of fun, and the museum of science in general/harry potter exhibit is awesome! if you want to do the harry potter exhibit, you might consider just buying a membership to the museum. its pretty reasonable, and brings the HP add-on ticket down to $5 per ticket. we went last weekend and it was really a lot of fun. and the museum itself is well worth a visit. I would not do the enchanted village a pp mentioned that is in avon right now. we did that this past weekend and it was fun, but a total time suck and if you are only here for a short time, stick to boston.
my kids are a similar age (7, 5, 5, almost 8, 6, 6) and their favorite things to do in boston include the museum of science, the institute of contemporary art, the aquarium, faneuil hall (hanging out and watching the street performers is a ton of fun for them), and certain parts of the freedom trail. they love the frog pond and the playground attached to it. Kings for bowling is very cute. they loved the trip to the top of the prudential center.