NY's fifth win in six games was supplied when Aussie Cahill met Juninho's free kick to score from close range for his fourth goal of the season.
Elsewhere, Sporting Kansas City were held 1-1 by DC United, while Real Salt Lake posted a 4-1 triumph over Chivas.
In Washington, Kyle Porter's first MLS goal on 65 helped DC United end a run of seven straight defeats.
Porter latched on to Chris Pontius's curling cross to slide home the equaliser which arrived just five minutes after Sporting KC had taken the lead.
At Carson, California, Ned Grabavoy netted in the fourth and 90th minutes as Real Salt Lake secured their third win in four matches.
Joao Plata and Robbie Findley also posted second half goals for RSL, while Jorge Villafana headed in Edgar Mejia's assist for a 55th minute consolation.