AE offers integration with 3d plugins and programs. C4D has a tight AE integration. Element 3D, the Mettle plugins, Zaxwerks are some of the major 3D plugins you can use with AE.
You should read the documentation on the Adobe site for in depth information.
In addition to what Ted says, After Effects has two 3d rendering engines built in. One is not being developed any more (called the ray-traced renderer) and the other one is being developed like crazy (and it's the Cinema 4D renderer). They both render 3d geometry in AE's 3d space.
After Effects isn't a full 3d program though. However, it does come with a "Lite" version of Cinema 4D. So you can do some fairly impressive stuff without buying a full-fledged 3d program.
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