I checked into this last year when touring with a long wheel based recumbent, which is similar in size to a tandem. I boxed the bike. I gave up on the idea after getting conflicting information depending on who I talked to with Amtrak or the bus companies. I'm glad I did because the bus I took was full, including the luggage compartment under the bus. That was after a ticketing agent told me it was a sparsely traveled route. It would be very hard to get an unboxed bike in the compartment. I ended up boxing and shipping to a bike shop, which worked well. On the return trip I was able to box the bike with 2 Amtrak boxes and take it on the baggage car of the train. This worked fairly well, but there are many things that can go wrong when traveling with a bike on Amtrak.

You might want to read the following:
http://www.crazyguyonabike.com/doc/?...c_id=4630&v=5K