McGrady was inactive because of a sore left knee, and Artest sat out for the fourth time in five games with a sprained right ankle, but the Rockets didn't need them against the Knicks, who scored only 31 points in the second half and shot 35 percent overall.
Houston led 46-45 at halftime and opened the third quarter with a 15-1 run when the Knicks missed their first 13 shots out of the break.
Tim Thomas sank a 3-pointer with 4:11 left in the third quarter to snap New York's drought, but Alston hit two free throws and Wafer scored again on Houston's next two trips to keep the Rockets in control.
Houston took a 77-59 lead to the fourth quarter after the Knicks went 5-for-21 from the field with three turnovers, got outrebounded 18-6 and mustered only 14 points in the third quarter. The Rockets outrebounded New York 60-38 for the game.
Thomas scored 18 points, Nate Robinson had 17 and David Lee added 14 points and 11 rebounds for his eighth consecutive double-double for New York.
The Knicks surrounded Yao whenever he touched the ball, so Scola carried Houston's offense early. Lee outplayed Yao at the other end in the first quarter, scoring 10 points in the first nine minutes.
Both teams struggled to hit shots in the second quarter, including a ragged 3-minute stretch without a single field goal for either side.
Yao put back two offensive rebounds and scored and Wafer sank a 3-pointer on a Rockets' fast break to put Houston up 42-36 just before the 2-minute mark of the half. Chris Duhon, dealing with flu-like symptoms, swished a 3-pointer and Lee hit two free throws to pull the Knicks within one.
Yao scored inside on two rare open looks, Wafer hit a mid-range jumper and Alston sank a 3-pointer during the Rockets' decisive spurt in the third quarter.
The Rockets play the Los Angeles Lakers on Tuesday and Houston coach Rick Adelman isn't sure if he'll have McGrady or Artest for that one, either.
McGrady scored 26 points Friday night in a win in Oklahoma City, but his status is day-to-day with his sore knee. Artest saw a doctor on Saturday and said he was going to talk to Adelman and trainer Keith Jones before determining when he would play again.
Forward Shane Battier returned for Houston after staying home for the Rockets' just-completed five game road trip because of inflammation in his left foot, an injury that's bothered him since the offseason. Battier had nine points and nine rebounds.
Including Saturday's game, nine Rockets have missed a total of 65 games to injuries this season.
