[2] On July 3, 2001, McRae was named head coach at Niagara, where he attended graduate school.
In comments on his reasons for accepting the job, McRae said, "One, my aspirations to become a head coach, and there aren't that many Division I openings that come up each year.
In both his second and third, Niagara qualified for the MAAC tournament by finishing the regular season in the top four of the conference.
The team finished third at the MAAC Tournament, but got the program's first postseason win, 16–7 over Manhattan in an elimination game.
McRae won his 300th game as a head coach on March 16, when Canisius defeated Ohio, 16–8.
As the third seed in the tournament, Canisius started off 2–0 by defeating second-seeded Marist, 2–1, and first-seeded Rider, 18–7.
In the championship round, the team defeated fourth-seeded Siena, 12–11, to advance to the 2013 NCAA tournament.
Seven of McRae's players at Canisius have been selected in the Major League Baseball Draft, most recently Garrett Cortright in 2013.
[15] McRae was named an assistant baseball coach at Virginia Commonwealth University on September 1, 2017.
[16] McRae was named as the 53rd head coach in William & Mary's history by athletic director Brian Mann on the afternoon of October 27, 2021.