A native of West Palm Beach, Florida, McGaffigan attended Twin Lakes High School, Palm Beach Community College and Florida Southern College. He was selected by the New York Yankees in the 6th round of the 1978 MLB Draft.
McGaffigan began his first season in professional baseball in 1978 with the Oneonta Yankees of the Class A-Short Season New York–Penn League and the Class A Fort Lauderdale Yankees of the Florida State League. He pitched to a 4–6 record with a 3.12 earned run average (ERA) and 36 strikeouts in 78 innings with the two teams.
For 1979, he was promoted to the Double-A West Haven Yankees of the Eastern League, where he went 10–6 with a 3.81 ERA and 113 strikeouts in 144 innings of work. He continued at Double-A in 1980 for the Yankees' new affiliate, the Nashville Sounds of the Southern League. McGaffigan led the circuit with a 2.38 ERA while accumulating a 15–5 record with 125 strikeouts over 170 innings. He was named to the postseason All-Star team and won the Southern League Most Outstanding Pitcher Award.

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