Between Acela and Regional, Acela wins for speed. Regional usually wins for price, but not always. The speed difference isn't such a big deal that it would decide it for me. I'd usually pick whichever is cheapest.

Baggage - you just roll it onto the train. There are luggage racks above the seats. They have plenty of room.

Booking - ASAP. It's not like the airlines where prices fluctuate. Amtrak prices are only based on how many seats are open, so they pretty much only ever get more expensive as the trip time gets closer. Also, book two separate single tickets, not a round trip ticket. It's much easier to deal with canceling only one of the two segments if you have to.

Other than that, if you're traveling while it's light out, sit on the left side of the train when heading to NYC (right side when heading to Boston). You get great views of the waterfront in CT. If you really want to see the NYC skyline, reverse that advice.