Bradley Wright-Phillips scored twice in the second half as the in-form Red Bulls rallied past Atlanta for their fourth consecutive win on Sunday.
Atlanta hit the front in the 26th minute via Ezequiel Barco and the hosts thought they made it 2-0 five minutes later thanks to Josef Martinez.
However, Martinez's goal was ruled out by the video assistant referee (VAR) for a foul in the lead-up.
The Red Bulls made the most of their lifeline as Daniel Royer converted a penalty three minutes before half-time following a foul on Wright-Phillips.
Wright-Phillips then scored two headers in the space of four minutes prior to the hour-mark to see off Atlanta, who had Gregory Garza sent off with 19 minutes remaining.
New York's triumph, however, was marred by injuries to Kemar Lawrence and Tyler Adams.
Atlanta's lead atop the East is only one point following two defeats in three games, with the Red Bulls only four points behind.
A second-half brace from Alberth Elis helped Houston to a 3-2 victory over the Chicago Fire at Toyota Park.
The Dynamo trailed 2-1 at half-time but an Elis double within 18 minutes extended Houston's unbeaten run to three matches.