[4] Mahoney was the player-manager for Harwich in the Cape Cod Baseball League in 1937 and 1938, and was an all-league selection at catcher, described as "a sterling player, a good throwing arm, a couple of speedy feet and a gentleman always.

Although the Red Sox continued to struggle at the MLB level through 1966, Mahoney's scouts and minor league farm system began producing players who would assume key roles in its 1967 "Impossible Dream" pennant drive: Jim Lonborg, George Scott, Rico Petrocelli, Tony Conigliaro, Reggie Smith, Joe Foy, Mike Andrews, Sparky Lyle and others.

[11] Mahoney, like general manager Dick O'Connell, also signaled a change in Red Sox policy by actively scouting and signing African American players.

"Under O'Connell and Neil Mahoney, Boston's increasingly colorblind farm system had never been more productive," wrote Glenn Stout and Dick Johnson in their book, Red Sox Century.

Before his death at age 66 in Chestnut Hill, Massachusetts, in 1973, however, Mahoney's scouts would produce Hall of Famers Carlton Fisk and Jim Rice, and other stars of Boston's 1975 pennant-winning team such as Rick Burleson, Dwight Evans, Cecil Cooper and Bill Lee.