I do think the Xbox 360 is best. It's a high quality controller and every emulator I tried supports it out of the box. The one downside other than having to buy a proprietary wireless receiver is the crappy d-pad. I've just gotten use to using the analog stick in old games. You could try the fancier Xbox 360 controller with the twisting d-pad.
The PS3 controller sounded like it would be great, but driver support is abysmal. I can't stand MotionJoy.