I don't know TB. Like you said, it was a small boat. He couldn't have had a bunch of chain or something similar to weigh him down without Fredo knowing or without possibly sinking the boat. Michael's house couldn't have been the only one on the lake. Someone could've witnessed the murder if he was close by and didn't go out to far. There's the possibility that Neri wasn't the only one involved. A cleanup crew could've been waiting near shore. Neri tells Fedo he has a good spot in a secluded cove, puts two rounds in him, pulls up to land where someone's waiting, load him up and dispose of the corpse.