Maybe someone can chime in on how to verify that you have the factory keyless entry - if so, I got my remote from Keyless-Remotes | Keyless Entry Car Remotes and Key FOBs
... it was about $40 if i remember correctly ... the instructions for programming it are under a sticky:
http://www.toyota-4runner.org/3rd-gen-t4rs/7501-programming-instructions-keyless-entry-remote.html