Generally speaking, an GPU is never as good as a good as a dedicated video card. Plus, I prefer Nvidia to the now defunt brand ATI (everything is now called AMD).
With Nvidia, you've got access to PhysX, Cuda, 3D Vision, and Surround technology.
But again, if you've got an onboard GPU from AMD, then I'm pretty certain that your mobo must be for an AMD CPU, so I'd stick with only one brand. Having an AMD CPU/motherboard and an Nvidia Graphics card (which I think works best with Intel -> AMD and Nvidia are competitors) might not be the best choice. But that's simply my own opinion.