I recommend doing a screencast with Quicktime -- this will give you the highest quality video which you can import into AE. From quicktime, you could either work with the .mov format, or export a new .mp4 file. I'm pretty sure AE accepts both.
Because screencasting + animating can be a computationally difficult process, I recommend closing everything but Hype, Safari and Quicktime when you do the recording. In Quicktime, click File > New Screencast.