Pontius dodged the raindrops at RFK Stadium to score twice in the first half and add another after the break, helping United (3-2-3) extend its unbeaten streak to six games.
The D.C. midfielder now has four goals on the season, while rookie Nick DeLeon added his third goal for the hosts, who moved past New York (3-3-1) to claim second place in the Eastern Conference.
Thierry Henry scored in the 72nd minute for the Red Bulls, grabbing a share of the MLS scoring lead with his eighth tally of the season.
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