Johnson, 23, hit .308 (76-for-247) with two homers, 30 RBIs and 30 steals in 68 games with Class A Burlington in the Midwest League. He will join low-A Savannah. Johnson is not on the 40-man roster.
Johnson was selected in the 25th round in 2012 out of the Washington State University.
Cowgill, 27, hit .180 with two homers in 61 at-bats during his brief Mets career.