McDonagh and Marian Gaborik each finished with a goal and an assist, while Brian Boyle, Ryan Callahan and Artem Anisimov also scored for the Rangers, who also secured the top seed in the Eastern Conference.
Henrik Lundqvist helped the Rangers claim their first division crown since 1994 with 37 saves.
New York also completed a six-game season sweep of the Flyers. The last time they accomplished that was in 1971-72.
Ilya Bryzgalov allowed five goals on 24 shots in his return from a three-game injury absence.