According to the fah people, there is a lot of optimizing left to do on both brands of card.
Also, as I understand it, the ATI card has so many more shader processors, but they aren't being fully utilized by the small molecules being tested in the early stages of GPU folding. The NVidia architecture is much better at the kinds of work that is being done at the present time.
Lot's of posts at the fah forum talk about ATI catching up with NVidia in folding production power when larger molecules start getting tested. Personally, I read these as wishfull thinking in large part, but I certainly don't know enough to say anything with authority.
But at present, when it comes to folding at home, no matter which two cards you compare, NVidia blows ATI production out of the water.... it's not even close.
-Sid