The best time to get rid of interlacing is during capture. I have a card that removes it in hardware but there's some quite sophisticated software de-interlacing available for capping with VirtualDub.
If you don't need a pile of video captures I'd just leave the de-interlacing through editing (Most editors seem to suck at this... (premiere...for instance)) then take care of it in Cleaner. Just make sure you select the right input profile before encoding (very important!!).