The issue is quite confusing, but the way I understand it is that from an IRS perspective your "Tax Home" is your domicile (BOS). This is what makes commuting expenses non-deductible among other things.
However from a State Tax perspective you pay taxes in your state of *residence*. Where you actually live. Residence is NOT the same thing as Tax Home.
So if you live in NH you should NOT have to pay MA taxes. I know a least a half dozen airline pilots who live in NH for exactly this reason.
Where the company is headquartered is irrelevant.