The 27-year old ended almost a two-month scoring drought when he nodded home Connor Lade's cross from the left in the 43rd minute before he double his sides advantage prior to the hour-mark with another header, this time from a Thierry Henry cross.
After the match, Cooper was thrilled with his performance and also explained his celebration which was a tribute to the son of former USA star Claudio Reyna, Jack, who lost his battle with cancer recently.
"I think it's important to always stay positive. I have so many quality teammates around me and I have so much confidence in them," he said of breaking his drought.
"You see today the opportunities that they're able to create for me and the two finishes were just yards outside of the goal and you see the great quality in the pass. I'm just happy I didn't mess it up for them."
He added: "After the goal, I wanted to pay tribute to Claudio's son. Claudio has been a personal hero of mine.
"He's been so important to US Soccer and also the team here in New York. It's obviously an incredibly sad situation. I wanted to pay tribute to his son and hopefully we were able to honor him and their family with our hard-working performance today."