Has something changed?
Espada III - I think that's a good call, or you could always take the train (direct service from central Boston to Newark airport, but takes nearly 5 hours), which your children might enjoy.
I've successfully avoided the US for the last few years, but it used to be the rule that you had to clear immigration at your first point of entry* and emigration at your last. Is this no longer the case?
* With a few special exceptions, such as Irish airports with US immigration facilities. Bound for SFO on a LHR-SEA-SFO, you had to go through customs and immigration at Seattle and v.v. on the way back. So it wouldn't be possible to do immigration at BOS on a BOS-EWR-MAN trip.