I think that'd very much depend on which exact cards are in question. I don't think anyone would complain about playing it on an 8800GTX, nor would anyone be too impressed playing it on an FX5200.
Both have high-end cards, and both firms' high-end cards will get you places.
Personally, I've upgraded to a GeForce 7800 specifically for this game, and can't say anything bad about it. Been a pretty (if incidentally) loyal nVidia customer for many years now, and for the most part they've kept me happy.
I should note that I hear of people complaining of ATI driver-related issues with the game, though I don't know about these directly. I personally haven't had any problems at all on my two nVidia cards with SHIV (6800 and 7800), and the game is very very stable.
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