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Born in New York and raised in Hoboken, New Jersey, Father Cooke received a bachelor of arts degree from Fordham University (New York) in 1960. He would also go on to receive a master's degrees in teaching and philosophy in 1962 and 1965 respectively from Fordham. Father Cooke furthered his educational pursuits by earning advanced theology degrees from Woodstock College (Maryland) in 1967 and Yale University (Connecticut) in 1968; and a doctorate from the University of Wisconsin (Madison) in 1971. His area of expertise focuses on ethics, the theory of knowledge, and the philosophy of language.
Father Cooke served as a provincial of the New York Province of the Society of Jesus from 1978-1984. From 1980-1984, he was the Chairman of the Higher Education Committee of Jesuit Provincials, College Presidents, and Rectors. He was also a delegate at the Jesuit General Congregation in Rome 1983.
From 1971-1976 and 1985-1991, Father Cooke taught Philosophy to graduate and undergraduate students at Fordham. In 1987, he became the director of the Collegiate Program of the Jesuit Scholastics at Fordham's Murray-Weigel Hall, a program for Jesuit students which leads to a master's degree in philosophy from 1991-1992, zacting president from January through March 1992, and executive vice president and professor of philosophy from 1992-1993.