After spotting Toronto an early 1-0 lead, the Red Bulls responded in the 13th minute when Markus Holgersson headed home Henry's corner kick.
Fourteen minutes later, Henry found Kenny Cooper for an open-net score, putting New York ahead to stay. The pair teamed up again for another Cooper tally in the 88th, building a 3-1 advantage.
Cooper assisted Henry in stoppage time for the final goal as the Red Bulls (15-8-8) moved into second place in the Eastern Conference with three games left.
Ryan Johnson found the net for Toronto FC (5-19-7).