I'm having a hard time supporting the Michael is the spy theory...

I think that if the people who are looking for Ben knew enough about the area to have some idea as to where the island is, they would probably find it weird that some random man and his son were floating around on a fishing boat in that obscure of an area (Sawyer even told Michael that that isn't the type of boat to take off shore more than about 100 miles). It seems like the first thing they would've thought would have been, "I bet Ben stuck him out here to find us and spy on us...." and at the very least, they probably wouldn't share any sort of relevant information around him.

Although, I can't think of a better suggestion as to who it is. It IS lost.....maybe they're both invisible or something and the freighties don't know they're on the freighter.