You might not want to wait on booking the bus - don't know whether it will sell out because April 4 is Easter (people making quick weekend trips?). Don't know about train, either, but seems less likely.

I went on the Megabus website, and it is not yet accepting reservations for April 4. I input the week of March 16th, and got a $90 total (Bost-NY $39; NY-DC $51) for the three of us from Boston-NY-DC! But, DH really wants to take the train, and we're saving lots of $ of these great hotel deals (and probably by not driving) so, the train it is.

For anyone still following this thread, we decided to drop the New York leg---may instead visit NY with my sister during her annual Thanksgiving visit to her MIL. So leave Boston on 4/5 via Amtrak to D.C., four nights in D.C. Now let's hope the Amtrak isn't still flooded out!