I used to fly the shuttle from BOS to LGA. Since 9/11, it is such an infernal pain that I've started taking the Acela. Hands down a substantially more pleasant experience, although it takes on average about 30 minutes longer door-to-door. Of course, this obscures the frequent long-tail events inherent in flying the BOS-LGA corridor, such that my minumum door-to-door is 2:15 (beats Acela's 3:30 or so), but the maximum can be counted in days if the weather conspires against you.

Unfortunately (or fortunately, depending on your thoughts on Amtrak), it seems a lot of other people have come to this same conclusion, and I have found the Acela to be quite full at times.