Although Tim Cahill almost instantly cancelled out Julio Morales' 30th minute opener, Chivas were back in front courtesy of Erick Torres' penalty on the stroke of half-time.
Torres then sealed it with a third goal in the 81st minute, with Dax McCarty's late goal not enough for New York.
However, the Red Bulls hung on to third place in the division as the Philadelphia Union suffered a 5-1 loss at the hands of the New England Revolution.
Danny Cruz equalised in the 51st minute after Kelyn Rowe put New England in front midway through the first half, but after Amobi Okugo's 58th minute own goal, further strikes from Rowe, Diego Fagundez and Juan Agudelo - three goals in nine minutes - put New England in complete control.
Okugo's afternoon deteriorated further in the last minute when he was shown a second yellow card to go with his own goal.
Clint Dempsey got a win on his home debut with the Seattle Sounders as Eddie Johnson struck on the hour to sink the Portland Timbers 1-0.