Who's paying? It really shouldn't matter if it's just cosmetic/body work, but if it's the other guy's insurance you can insist on the Toyota repair shop if you're more comfortable with that, but an indy should be able to take care of you just fine.
Dealers have no magical properties when it comes to their bodyshops. I say take it to a shop recommended by friends or family. Then take a look at the shop and the cars in the repair process. You will recognize a quality repair facility when you see it and talk to the personnel.