LGA-BOS works because Amtrak has to share with Metro North, and the Acela is frequently delayed during rush hour as a result.
Between DC and NYC though, Amtrak doesn't have that issue, and the train beats flying in almost every situation. I'm surprised that the shuttle has held on this long. If the Hudson tunnels take a turn for the worse flying will make a resurgence but right now the Acela is king.