This appears to be a bit buggy at the moment. An hour into and I can not find him. He is supposed to be on the deck of the ship somewhere. If you can't find him soon, come back to it later. (as of 9-dec-10) good luck =)
Ok, fly away from the shipped so you arent tracking with it and fly back to ship. Seemed to work, also a few people looking for him as well.