Johnson, 23, was batting .310 with with a .414 on base and had 16 doubles, three triples, two home runs and 30 RBI in 67 games for Single-A Burlington. He also had 30 stolen bases.
The right-handed hitting outfielder was drafted in the 25th round of the 2012 Draft from Washington State University. He will be assigned to Low-A Savannah.
Cowgill, 27, was designated for assignment after batting .173/.189/.327 in 53 plate appearances for the Mets this season.