Boston, MA is great and has tons of historical sites and all kinds of museums and whaling tours. It also has the top universities and they have exhibits and museums of their own. You may try the MIT museum for hands on activities with your kids.
There are a number of frum shuls in the Brookline/Brighton areas (2 miles from Boston/Cambridge) and some kosher restaurants and pizza places.
For accomodations, you may try the Waltham area, which is about 6-7 miles from Brookline/Boston, but the hotels are much cheaper. If you are traveling during the week, it won’t matter, since you can drive to the shuls or restaurants in about 15 minutes. However, if you will be over Shabbos, then you don’t want to be in Waltham, and would be better off in Brookline of Brighton. Many families will be happy to have guests eat with them for Shabbos, and you can contact the YI of Brookline, and they will put out an email, or just show up in shul on Shabbos, and they always announce that there are willing hosts if anybody needs a place.
There is a Holiday Inn close to the YI which has special room locks for frum people, but is quite expensive.