It is a massive blow for McCartney who came off the bench in the 78th minute to make his first appearance since suffering medial ligament damage in his knee four months ago.
The full-back hobbled off in injury time after suffering the same problem.
"I would have thought he will miss the rest of the season," Hammers boss Sam Allardyce said.
"It's a recurrence of the same injury, his medial ligaments, which is a very big disappointment for him and for us. We are disappointed for him because he has waited so long to get back, and get on the pitch.
"We thought we would give him a run out and give the lads who had done so well a rest, but sadly he went down with the same injury."
At least the three points were some consolation as an Andy Carroll double and Gary O'Neil's strike steered the London side up to 11th and six points from the drop zone.