This is the part I don't get. It's a river, not the ocean. Drive the trains to the closest station on the New York side (New London, just before the bridge), put everybody on busses, go to Mystic 9 miles up the road, and catch a train from there to Boston.
They could easily time the trains to all get in at the right times. Granted, wouldn't be the best possible service, but it's considerably better then nothing or this limited bus thing they are doing.