The faster Amtrak will be welcome to travelers on the BOS-NYC run. It will in fact be close to the Shuttle on a downtown Boston-midtown Manhattan basis (once one adds ground transport, ssecurity, etc. to air, making for 2+ hours door to door), far less hassle, and cheaper. And in winter it is not as subject to weather delays (even after 6 years in Boston I'm still mystified at how Logan seems to turn to molasses every time it turns overcast). The new train also will reportedly have laptop jacks, and more leg room than the Shuttle (Delta or USAir) to NYC. These are all clear value-added benefits, and if they can hold the price constant I would expect that ridership will climb.
Example of Amtrak's continued value in the northeast: in January I was running a large (500-person), high-profile conference, with probably 20% coming from NYC. Of course this was the day every airport in DC ,NYC, Boston, etc. was closed due to snow--but a surprisingly large number of savvy participants made it only a few hours late by taking the older, slower Amtrak. if they ahd planned their schedules from the start with the faster train, they might have arrived on time....