Scott Atchison came in to face pinch-hitter Howard, who greeted him by blasting a 2-0 pitch off the base of the center-field wall, driving in both runners.
Chase Utley followed with an RBI single and the Phillies went on to take their third straight from the Mets.
Cole Hamels (1-3) collected his first win of the year despite allowing six walks. The left-hander yielded one run on two hits while striking out eight.
Niese surrendered three runs (one earned) on five hits over 6 2/3 frames.
David Wright supplied the only RBI for New York, which fell for the sixth time in eight games overall.