Jesus Medina put the Boys In Blue ahead after just five minutes and Taty Castellanos added a second in the 65th minute as NYCFC took all three points back to New York.
Story of the match
NYCFC had their first chance after just 44 seconds as Castellanos got behind the Philadelphia back line, cut in and drove a shot straight at Union goalkeeper Andre Blake.
The visitors were on top with their next chance as Maxi Moralez led a counterattack after winning back possession, passing it to Medina, who slipped it in for Anton Tinnerholm.
The Swede quickly worked it back to an unmarked Medina and he beat Blake for his sixth goal in his last eight MLS appearances.
Things got even better for the Boys In Blue after Philadelphia was reduced to ten men in the 16th minute following the dismissal of Jose Martinez for violent conduct.
Making the most of their numerical advantage, Moralez passed out wide to Gudi Thorarinsson and his pass found Castellanos at the back post, but he couldn't keep the shot down.
In the 27th minute, Castellanos had a header that he put too much power on and Moralez forced Blake into a fabulous save, tipping over the Argentine's effort.
Medina then fired just wide and with three minutes left in the half, Philadelphia finally produced their first chance when Santos' free-kick went well wide of the right-hand post.
As the second half began, NYCFC picked up where they left off as Moralez again forced Blake into tipping a shot over, this one from distance.
Controlling the game, especially possession of the ball, the Boys In Blue doubled their lead as Castellanos took advantage of a poor back pass, rounded Blake and finished the chance with a rabona.
The Argentine almost added a third ten minutes later as his curler whizzed past the post. Tinnerholm and Castellanos missed chances to add a third, but NYCFC had done more than enough to secure an impressive victory.
Man of the match: Jesus Medina
This could have gone to just about anyone. Tinnerholm controlled things down the right hand side, Castellanos was a constant threat, but Medina has now turned in consecutive MOTM performances and his goal after brilliant build-up play showed why he's one of the most dangerous players in MLS at the moment.