I take the train into NYC with some regularity from South Station/Back Bay Boston. I've had no luck with bringing my regular bike on an Amtrak train. The last time I rode down to South Station with my folder I ended up leaving it locked at the station because the woman taking tickets for the Acela said it was not allowed even as carry on baggage- and that was my
folder!
Unfortunately, my experience has been that Amtrak is generally bike unfriendly and inconsistent in it's policies and/or their interpretation by employees. I think the don't ask/don't tell policy of just folding your bike up and getting it on the train without asking anyone- may be the best option at present. I think a bag for the folder would make it all the easier. It just feels a bit immature and insulting to be paying the ticket prices that Amtrak demands for the trip to NYC and have to play such stupid games getting your bike on the train.
I say a letter/email writing campaign is in order.