This isn't really relevant to After Effects. After Effects doesn't take much advantage of the graphics card.
If you're using Premiere Pro CS5, then the graphics card matters much more.
I recommend asking video card questions on the Premiere Pro hardware forum:
One thing the Premiere Hardware forum will tell you is that a PC runs Premiere Pro much better than a Mac, which is true. Apple has decided not to offer NVidia cards this time around in their new Mac Pros. Speculatively speaking, this might be due to Premiere Pro being competition to Final Cut and supporting NVidia cards would promote the switch to Premiere Pro in effort to have faster performance. Not to say you couldn't go out and buy your own NVidia card and install it, but that is out of the range of my knowledge.
As for After Effects, this means nothing. AE doesn't use this Mercury Playback Engine, so what card you have doesn't matter so much. I would browse through the Premiere Hardware forum and see what you think. They will persuade you to switch to PC for performance gains. It just depends on what you are willing to sacrifice I guess, or gain. A similarily performing PC will cost you less definitely, but that's not the reason why people use Apple stuff
Thanks for the answers so far. I'm aware that AE won't use the Mercury Engine, but I'm setting up the new mac now and wanted to get only the best components available. So I was a little bit surprised that the best graphics card you could buy in the apple store is around 450 Euros and the Nvidia card is around 1700 Euros. Don't get me wrong - I'm not comparing the cards based on their price, but it is hard to compare the cards based on their hardware specifications, cause both companies use their own crazy, hyper-hyper marketing words. So I'm wondering why the Nvidia card is that amount more expensive?
I decided to spend my money in 32 GB RAM. Should be the best decision for AE and Foundry Nuke use...I hope!