Niese (2-0) surrendered five hits over 6 2/3 frames, allowing one walk and striking out five for the Mets, who continued their surprising start by clinching their three-game series with the Phillies.
Bobby Parnell and Jon Rauch finished up the whitewash with two scoreless frames as New York improved to 6-2.
Phillies starter Vance Worley (0-1) was tagged for four runs on eight hits over a six-inning effort, issuing four walks while striking out five.
Philadelphia fell to 3-5 to start the season.
Notable deaths of 2014 [PHOTOS]
Michael Sam cut from the Dallas Cowboys