Well, Independence Air also flies between Boston Logan and New York JFK
, and if you join i-club, you can get a $25 off on your first RT.
I personally like ACELA Express -- downtown Boston to Manhattan New York... Unlike regular Amtrak, ACELA is pretty pleasant.
If you insists on flying, I prefer DL
Shuttle over US Shuttle -- DL
Shuttle has an open seat policy and the service is nice with snacks (real snacks, unlike pretzels served by US Shuttle). Seating is nicer than US's regular Y.