Caveat emptor: go with a reputable brand and you should be OK with either GPU.
My experience has been the exact opposite of pinot's. Issues with ATI card fan motors exploding (yes, exploding, as in the fan hanging by the wires, scorch marks on the heat sink and bits of capacitor flung around the inside of the case), lots of artifacting (hash marks, tearing with vsync enabled, terribad issues with gamma correction causing atrocious washout even at low settings, etc.) heatsink bonding problems and PSU/slot compatibility problems, where NVidia cards fixed all of these. This includes a recent 5870 card I bought.
Your mileage may vary.
In all fairness, two different manufacturers' 6970 cards are not alike, which is the same with two different manufacturers' GTX580 cards. Different firmware loads, different assembly plants, different memory parts/capacitors/heatsinks/etc. I've become a big fan of EVGA cards now that BFGTech is out of business, and have yet to see any issues with their NVidia cards.
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