I   would export png format via the queue manager. This format is uncompressed and will leave a transparent background as an alpha channel if you desire.
Its been awhile since I have used After Effects, but every video application can import an image sequence.
I tend to assemble my image sequences in Photoshop CS4 Extended, but only because it is quick and easy  to import the sequence, change edit the background drop a logo layer in front and export as a .mov ( I am on a mac and prefer quicktime as my delivery platform) At this point the movie is still uncompressed which is important. I wouldn't add any compression until the last stage , which will be saving file for web delivery. So if you plan on exporting to flash. make sure the video going into the flash video conversion is uncompressed. if it is already compressed you end up with double compression and a lesser quality end result.
This is another reason to export image sequence over a quicktime movie. I tend to only render to a quicktime movie when I a doing proof and don't mind tying up poser for a little bit. most of the time I still send those lesser quality firefly renders to the render queue so I can keep working and quickly assemble them in Quicktime Pro  to check the proof.

anyway, hope that helps some.
JC-