Toronto won for the third time in four games, overcoming a five-point deficit to start the final period and holding the Knicks to 12 points during the closing 12 minutes.
Jonas Valanciunas contributed 16 points and 18 rebounds for the Raptors while Kyle Lowry had 15 points.
The Knicks were limited to 37 percent shooting and made 10 fewer free throws than did the Raptors.
Andrea Bargnani had 18 points and 12 rebounds to lead the Knicks, who have lost three times in four games.
New York played its second straight contest without Carmelo Anthony, who is suffering from a sprained left ankle.