There have not been many problems in Boston outside of the downtown area where protestors go. The airport is near downtown, but in an ethnic neighborhood that is less likely to have anything to do with protestors.
Your biggest challenge in Boston is the traffic and how complicated the roads can be. Unless you have a good reason to visit the main part of the city it is easiest to go to and from the airport from the north, using US-1, Rt. 60, and Rt. 1A.
Get 86 in Pa, across the Southern Tier then up thru the Finger Lakes. Longer, yes, wildly more beautiful, absolutely. Far less boring, less traffic and fewer tolls on the thru-way.