In 1972, his final season at Montclair, the program appeared in its first NCAA tournament, finishing third in the East Regional.
In Cooney's four seasons at Montclair (1984–1987), the Red Hawks went 138-50-2, reached four Division III College World Series, and won the 1987 national championship.
It beat Eastern Connecticut, UC San Diego, and UW-Oshkosh to advance to the championship game, where it defeated Oshkosh, 13-12 in 10 innings.
[9] Prior to the 1988 season, Division II Florida Atlantic (FAU) hired Cooney to replace Steve Traylor, who had left to become the head coach at Duke.
[10] Cooney held the position for 21 seasons, leading FAU to Division I, seven NCAA tournaments, and a 742-480-5 overall record.
[12][13][15][16][17] The Blue Wave returned to the NCAA tournament in 2000, then made their deepest postseason run under Cooney in 2002.
(Of Cooney's six Division I Tournament appearances at FAU, 2002 was the only year in which the Blue Wave were not placed at the Coral Gables Regional, hosted by nearby Miami.)
[13][15][20] During Cooney's 21 seasons at FAU, the program had 58 selections in the Major League Baseball Draft.
Other of Cooney's players to appear in Major League Baseball were Tim Harikkala, Carmen Cali, Tommy Murphy, Michael Crotta, Mickey Storey, and Jeff Beliveau.
His oldest son, Jim, pitched for Cooney from 1999–2002, was drafted by the Baltimore Orioles, and played three years of professional baseball.
[24][25] Since retiring from coaching, Cooney has moved to Sweetwater, Tennessee and started business ventures in farming, antiques, and Christmas tree growing.