Besides the mainstream shops names above I've had very good luck with.
Sidetracks: www.sidetracks.net Some brass, SHS, AM and SSA RTR plus more.
Chicks Hobby Shop: http://chickshobbyshop.com/ Good inventory of PRS kits.
There was another fellow in the San Diego area who had a lot of "S" scale PRS kits, SHS cars and locos and AM passenger cars...among other items. I think it was Whistle Stop but they didn't have a website.
Good Luck!
Butch