Flaherty was the first in a long line of outstanding linebackers developed at Holy Cross during the Carter-Duffner era. A four-year starter for the Crusaders, he served as a tri-captain of the 1983 squad which won the Lambert Cup championship and advanced to the NCAA Division I-AA playoffs for the first time in school history. Flaherty was selected as the team's Most Valuable Player in 1983, in addition to being a two-time Davitt Award winner.
A third team All-American in 1983 and an honorable mention All-American in 1982, Flaherty also earned All-New England honors in both his junior and senior seasons. He graduated as Holy Cross' all-time leader in career total tackles with 447, and set what was then a single-season record with 152 tackles during the 1983 season.
Following his graduation, Flahery played in the National Football League for the Philadelphia Eagles and the Dallas Cowboys, and in the United States Football League for the Tampa Bay Bandits. He also did work in substance abuse counseling and with the Fellowship of Christian Athletes.