Baker was a two-year member of the Alfred State College baseball team. He helped the Pioneers to an 82-34 record, two WNYAC championships, and a Region III championship.
For his career he hit .387 with 24 doubles, nine triples, six home runs, and 85 RBIs. He scored 115 runs in a total of 116 games and was 42 for 47 on the base paths. In 450 defensive chances, mostly at second base, Baker made just 23 errors.
Currently, he is ranked 5th all-time at Alfred State in stolen bases, 6th in career batting average, 7th in triples, and 10th in runs, hits, RBIs, and total bases.
Baker was a two-time All-Region, All-WNYAC, and ASC Most Valuable Position Player selection. He was named the NJCAA Division I Defensive Player of the Year following the 2001-02 baseball season, and was named the Alfred State College Senior Athlete of the Year in 2003.
Following his career at Alfred State, Baker transferred to Mansfield University where he had a solid career. In 2005, he led NCAA Division II with a .500 batting average and was drafted in the 28th round by the Houston Astros becoming the fourth Pioneer to be selected in the major league baseball draft.