As part of a corp relo, we shipped our cars from Boston to San Francisco using
http://www.autolog.net/
They were very good, and the cars are shipped in covered rail I believe. In fact, I believe they are based in NJ, and have depots in NorCal and SoCal. If I remember correctly, our car was taken by truck to a depot in NY/NJ, and then shipped by rail across the country, and it ended up at a depot in the East Bay. Arrived without a scratch.
I also shipped another car on our own using them, and we paid out of pocket for that one (Boston to Bay Area as well), and it ran about $850.
Update: I just went to their site, and they have an instant rate calculator. I stuck in a zip code for Astoria and one for Burlingame (near SFO), and it said $975.
Mike