Mueller attended Stillwater High School in upstate New York, where he played baseball and basketball. Mueller won a state basketball championship in his senior season, 1988. He was offered a basketball scholarship at Siena, but chose instead to attend Eckerd. He played both basketball and baseball at the Florida college as a freshman and sophomore but focused exclusively on baseball as a junior and senior. He graduated in 1992.
After getting his master's degree from Saint Rose in 1994, Mueller began a seven-year professional baseball career spent entirely in independent leagues. From 1994 to 1995, he played for the Marshall Mallards and Will County Claws in the short-lived North Central League. Partway through the 1995 season, he returned to upstate New York, where he played for the Adirondack Lumberjacks from 1995 to 1996 and the Albany-Colonie Diamond Dogs from 1997 to 2000. Primarily a first baseman and an outfielder, Mueller had a career .286 batting average and hit 76 home runs.
Mueller's first coaching job came with Saint Rose from 1993 to 1994, where he worked as an assistant while getting his master's degree.
Mueller was hired as Albany's head coach the following season, the Great Danes' first in Division I. Playing as an independent, they went 19–24. After the season, he played his last season of professional baseball. Albany joined the America East Conference for the 2002 season. In 2004, the team went 37–14 and tied for second in conference. It appeared in its first America East Tournament and Mueller was named the conference's Coach of the Year.