When you talk about 3d in AE, what do you mean?
Are you referring to using CS6's obsolete ray-traced renderer, a third-party option (like Element 3d, Zaxwerks 3d Invigorator, or Mettle's Shape Shifter), or are you referring to the brand new Cineware effect?
If you're talking about the ray-traced renderer, the GPU matters a lot and you haven't mentioned what's in your machine.
If you're talking about a third-party option, then it depends on the option.
If you're talking about Cineware, your CPU is of the utmost importance.
A MacBook Pro would be a poor choice. It will work (depending on the specs), but you tend to get more power for your money in a desktop or workstation vs. a portable computing option.
Szalam's advice is good.
In simple terms, you need lots of RAM, a fast CPU with multiple processor cores, and at least one very fast disk (preferably an SSD) for your disk cache. The GPU matters very little, with the exception that Szalam mentioned.
See this page for information about hardware for After Effects: http://adobe.ly/pRYOuk
I'm mainly working with Element 3D an object based particle engine plug-in. Really in the end, I am just looking for the typical mac pro hardware setup used by professionals who use AE. Thanks!
Element 3D uses OpenGL, and it benefits from having a large amount of VRAM on the graphics card, as mentioned here:
Check out VideoCopilot's list of video cards and how well they perform (link is available at the page Todd shared).