Cowgill, the former piece in last offseason's Trevor Cahill deal between the Athletics and Arizona Diamondbacks, played in 38 big-league games last season. The 26-year-old utility outfielder hit .269 with one home run and nine RBI.
However, most of Cowgill's playing time came with Triple-A Sacramento, where he put up big numbers in 2011.
Cowgill, who bats right and throws left, was drafted in the fifth round of the 2008 Major League Draft by the Diamondbacks. The former Kentucky Wildcat earned third-team All-American honors by Rivals.
Marte, 21, was named to last year's Eastern League Mid-Season All-Star Team with Double-A Binghamton. However, the Mets locked up David Wright with a long-term contract this offseason, so the need for the Mets to develop a corner infielder is no longer a necessity.