Boston has the "downeaster" to Portland Maine. No boxes necessary but you do need reservations.
Bikes on the Vermonter was scrapped years ago, Ny & Vermont were paying (I seem to remember) for the baggage car. For the most part with Amtrack (North East), you can't get there from here.
When I went to Boston, I had to have family drive me to Worcester, so I could get my bike on the commuter train off peak.