While we have week by week voting on the MOTY/GOTY nominations, I thought the short list and final selections were done by a panel, rather than public vote. I don't think it has always been by public vote.
Despite Joe's being a great mark, I thought Howe's nomination was comparable, but his sustained repeats through the season (all of them would have been worthy nominations) made him worth the win.
I was equally surprised by Buddy not winning GOTY — perhaps people thought he really did run too far before his kick.