The modest NVIDIA cards work amazingly well on the Mac as long as they are on the list. There's a comparison spreadsheet of all compatible cards on the net somewhere. I haven't got time to dig up the link for you now but it's refered to in one of my posts on this subject.
As for the new MacPro and ATI, we'll have to wait to see what the future holds on that end.
the raytracer uses nVidias Optix engine so the raytracer as it exists today will never run on ATI hardware.
as far as 3d goes AE v12 has cineware which uses yoru CPU to do the rendering.
The GPU acceleration of the ray-traced 3D renderer is the only thing in After Effects that requires an Nvidia GPU. Every other GPU feature works fine on AMD cards.