Not sure about the details as I know very little about After Effects, but a quick google indicates that it can respond on MIDI for controlling stuff. So I'd look at something like LoopBe (an internal MIDI bus) and set up your controller tracks in Reaper, using LoopBe as your MIDI output on the I/O of the controller tracks, and setting After Effects to respond with LoopBe as the MIDI input.
http://www.nerds.de/en/loopbe1.html