10 years ago I would have said MHT for lower fares and easy in/out. Now, BOS. The fare advantage MHT used to have has IMHO disappeared. Frequencies are fewer, which means fewer irrops options for you. And TSA at MHT is in my experience very difficult to deal with. (Enplanements at MHT have been falling like a rock in recent years, for all these reasons and more. Pretty quiet there nowadays.)
Advantage BOS. And Nashua isn't 50 minutes away from Logan unless it's evening rush or bad weather... more like 30-35.