Ditto to the MFA and the glass flowers; Salem is a cool day out, and Wenham museum has a massive toy collection, with lots of old dolls in period costume.
In New York, the Met is amazing (of course), but my favourite museum is the Frick Collection, which is a couple of blocks away - an oasis in Manhattan.
Are you hitting New Hampshire on your way? Because in Manchester NH, there are a few Frank Lloyd Wright houses close to one another, and one is owned by the local museum, so you can do a tour: http://www.currier.org/collections/zimmerman.aspx
Have fun!!!