MacArthur one-timed a pass from Mikhail Grabovski at the crease and Islanders goalie Al Montoya grabbed it, but a video replay showed his glove was over the goal line during the snag and the game-winner was upheld.
MacArthur also notched an assist and Grabovski collected a goal and three helpers for Toronto, which won for the third time in four games.
Jake Gardiner added a goal and an assist and Jonas Gustavsson made 29 saves in the victory.
PA Parenteau, Josh Bailey and John Tavares netted the Islanders' goals.
Montoya finished 17 saves for New York.