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In fact, if you're going from Boston to NYC (insteasd of the other way around) there's a $40 round trip special. And on some runs you even get a movie.
I should add however that though you don't want to jostle around in a bus or train after a long flight, that the shuttle is not quite a first class experience. It is cheap, single class, fast, and regular; it caters to business travelers. And the non-shuttle flights are likely to be even worse, because they will use small (e.g. 19-seat) regional jets or turboprops instead of airliners.
If I order far enough in advance, I can fly round trip DCA-LGA-DCA for as little as $98. Cheapest, slowest Amtrak round trip fare (my worst trip was 4 1/2 hours and I think 13 stops) OTOH is still over $160. Since you are already at JFK, moreover, the convenience of taking the train is lost, since you'd have to take the subway or a taxi into Manhattan (10-minute bus ride to the subway station, then 45 minutes or so on the A train to Penn station).