Howard was held to just eight points and eight rebounds.
Orlando has now lost five straight games for the first time since 2007.
Van Gundy made his instantly viral comments hours before tip-off Thursday. They flew in direct conflict with previous denials by Howard throughout the season that he'd made any kind of request about his coach to Magic management.
Howard continued to deny it Thursday, just like he did previous reports earlier this year that his signing with Orlando long-term was contingent on both Van Gundy and general manager Otis Smith's departure. Van Gundy's current contract runs through the end of the season.
Still, the morning's drama cast a definite pall over the game, which was controlled by the Knicks throughout the night.
After giving the Magic a 22-point beating 7 days prior, New York again was the aggressor and took a 17-point lead into the fourth quarter.
Playing again without injured center Amare Stoudemire, the Knicks built their lead drilling shot after shot from beyond the arc.
In other games *
At Auburn Hills, Mich., Greg Monroe had 18 points and seven rebounds, Rodney Stuckey scored 15 points in his return from injury, and Ben Wallace made five key free throws down the stretch as the Detroit Pistons beat the Washington Wizards, 99-94.
* At Chicago, Luol Deng had 26 points and Carlos Boozer pulled down 14 rebounds to lead the Bulls over the Boston Celtics, 93-86.
* At Sacramento, Randy Foye scored 20 points to lead the Los Angeles Clippers to a 93-85 over the Kings, who got 17 points from Isaiah Thomas.