Scheffler was playing alongside his fellow American in the final group and trying to overhaul a six-shot deficit in order to win the career grand slam.
That ensured there was a lot of support for him while every error Clark - who did his public persona no favours when he damaged a locker at last year's event at Oakmont after missing the cut - was jeered by some fans, some of whom were eventually thrown out.
Clark went on to win by one from compatriot Sam Burns, his second title in four years.
Last September crowds were criticised for their abuse of European players during the Ryder Cup at Bethpage, some 60 miles west and closer to New York.
"The crowd was tough today. New Yorkers, they are tough people," said Scheffler, who finished four shots behind in a tie for fourth.
"There was a good turnout from the fans. You like seeing the fans cheer for you. I think sometimes it can get a little too much when balls are kind of going off greens and you start hearing cheers. That felt a bit much to me.
"But at the end of the day, I can't control fan behaviour. Being in the arena is not for everybody: there's been crowds that have been for me in my career; there's been crowds that have been significantly against me in my career.
"I think Portrush (where he won last year's Open) was a scenario for me where Rory (McIlroy) is in Ireland, not far from where he grew up. Crowds can be tough.
"I think it shows a lot about Wyndham, how he handled not only this golf course but I think the crowd today as well and is a well-deserving champion."
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