If Amtrak has a freight service then that is news to me.
It does, but not between all points:http://www.amtrak.com/servlet/ContentServer?c=Page&pagename=am%2FLayout&cid=1241267371736
Regular bicycles and unicycles may be shipped on Amtrak Express. Bikes must be securely packed in a box; you may bring your own box or purchase one at the station (call ahead for details and to make sure that boxes are available). Bicycles are generally exempt from Amtrak Express size requirements."
You can only bring your bike on board with you between stations with checked baggage service. I suspect the same rule applies to Amtrak Express service.
IMO, if you are brining more than you can carry with you on the plane you are likely bringing too much. Use one pannier as your carry-on (or tape two together). Put the rest of the gear in a duffle and check it. Mail the bag home when you arrive. The only thing I would ship is my stove and fuel bottle to eliminate the risk of confiscation by the TSA.
Having your gear ahead of time gives you an opportunity to become familiar with it, and I doubt the checked baggage fees will be less than the cross country shipping fee.
As for the bike, with what most airlines are charging now, it's often cheaper to ship the bike UPS or FedEx. We typically go throuigh a LBS. Seems like they can get you a better commercial rate. While it adds costs, we have our LBS box our bike, ship them to a LBS at the start and have them assembled and tuned there. Saves us work, which is nice when you have just spent over half the day travelling and have to hit the road early the next morning.
For all, it's my understanding that Southwest recently uppped its bike fee to $75.
I live in Philly and am very familiar with the Atlantic Coast route from around Otisville, NY down to Conshohocken, PA and possibly a bit south of there. (I don't have the map for the section south of Conshy.) Just rode the stretch between Port Jervis, NY and Philly earlier this spring as I did last year. These were taken between Port Jervis and Milford, NJ, with a detour en route to a campground and wolf preserve:http://www.flickr.com/photos/davez2007/sets/72157633368316419/
Feel free to send me a PM if you would like detailed info. on the route, sights, services, etc.