Thor wins.
YJ is not a god, he is the future king of Kemteron
http://www.alphaflight.net/character_overviews/yukon_jack/
They are extremely long-lived, and his ultimate bone move is very strong but Thor has more versitility. All though his bone attack [yeah I choose those words] did cut through metal pretty easily so against Thor's durability...up to you to decide, since we never saw his full power or all what he can do.
That series of Alpha Flight sucked.