Encode through Media Encoder directly sent from AE (with audio of course). Use a high bitrate H264 (60Mbps for example) and upload that to YouTube where it will be re-compressed by them anyway to a 6 Mbps H264.
[Matteo Ferreccio]"I just finished a 1 minute commercial entirely animated in AE. My master copy is a PNG sequence, plus an audio track of course."
PNG is relatively slow to encode. Your renders will speed up a bit using QuickTime Animation Codec or TGA sequences (both have run-length encoding and will give small file sizes for imagery with large areas of flat color). Unless you're rendering 16b PNGs, the output from any of these would be identical, pixel-for-pixel.