The first thing I would suggest would be to copy the Cutout filter from the Photoshop filters folder and place it into the AE plug-ins folder. This will cause the filter to show up in AE. There's a certain voodoo element as to whether or not this will werk (lighting black candles and sacrificing a goat or two may help...) Sometimes it does - other times it'll just crash your komputer. If it werks, set it up and let it run - note that keyframing is not implemented on photoshop plug-ins, though.
Option 2 is to export your footage for treatment in Photoshop. You could export a Filmstrip file (yay! my favourite!) and run the filter on that, although, depending on the length of the clip, this could generate a huge file.
Probably, the best way I can think of do this is to export your clip as a series of images (bmp's or Tiffs) into a folder and run a batch in Photoshop. This is really quite straight forward - you can find details of how to go about it in the Photoshop manual or on-line help.
PsiPhi