An Anglican priest, he served as the President of King's College (predecessor of today's Columbia University) from 1763 to 1775, and was a public opponent of the American Revolution.

Ordained as a priest in the Church of England in 1761, he attracted the influence of several high clergymen, including Thomas Secker, Archbishop of Canterbury, who recommended him for service in the American colonies.

His pamphlet A Friendly Address to all Reasonable Americans on our Political Confusions; in which the Necessary Consequences of violently opposing the King's Troops, and of a General Non-importation, are fairly stated was later answered in best-selling tracts by Alexander Hamilton and Charles Lee.

For his Loyalism, Cooper, along with other prominent New York Tories, were issued death threats admonishing them "to flee for your lives, or anticipate your doom".

Of Cooper, in particular, this party evidenced a desire of "seizing him in his bed, shaving his head, cutting off his ears, slitting his nose, stripping him naked, and setting him adrift".