In 1987, Stein coached the Rockledge High School baseball team, leading them a district title with a 17–11 record. Stein was hired as the manager of the Class A-Short Season Little Falls Mets of the New York–Penn League in 1988. Little Falls were minor league affiliates of the New York Mets. In his first professional season as a manager, Stein led Little Falls to a 39–36 record. Stein commented that when he became a manager it was difficult to learn pitching after all the years of being a position player. In 1989, the New York Mets fired Butch Hobson, the manager of the Class-A Columbia Mets, and promoted Stein to that position. At the helm of Colombia that year, Stein led them to a 73–67 record. He also served as a player-coach with the Orlando Juice of the Senior Professional Baseball Association in 1989.