The teams will meet again Jan. 2 in the annual Winter Classic, which will be played outdoors at Citizens Bank Park -- home of the Philadelphia Phillies.
New York won its fourth in a row and moved into a tie with Philadelphia for first place in the Atlantic Division. The Rangers have a game in hand on the Flyers.
After a scoreless opening period, New York took a 2-0 lead in the second on goals from Derek Stepan and Ruslan Fedotenko. Marian Gaborik added to the advantage 1:48 into the third with his 21st goal of the season and the Flyers could climb no closer than a two-goal deficit the rest of the way.
Philadelphia has lost in each of its last three trips to Madison Square Garden. It was only the fourth road loss in regulation for the Flyers this season, fewest in the league.
Ilya Bryzgalov allowed all four goals on 24 shots.