Hamilton was traded to the New York Mets with Chuck McElroy for Rigo Beltrán, Brian McRae, and Thomas Johns on July 31, 1999. He played with the Mets through the 2001 season. In his three seasons with them he played in 150 games and hit .283. Hamilton and the Mets played in the post-season in both 1999 and 2000. In 1999, the Mets made the playoffs as a result of winning a one game playoff against the Cincinnati Reds. Once in, they defeated the Arizona Diamondbacks in the 1999 National League Division Series before losing to the Atlanta Braves in six games in the National League Championship Series. Hamilton had six hits in 17 at-bats in that series.