Harkness was the head coach of the men's ice hockey team at Rensselaer beginning with the 1949–1950 season through the 1962–1963 season. He led the team to a record of 176–96–7 and NCAA tournament appearances in 1953, 1954, and 1961, winning the NCAA title in 1954. His 1951–52 team averaged 8.28 goals per game, an NCAA record which stands today. He would leave the lacrosse team in 1958 to focus on RPI hockey after leading the team to a record of 112–26–2 in 14 years, and left RPI hockey in 1963 after three NCAA appearances, two Tri-State titles, one NCAA championship, and a record of 176–96–7 over 14 years.