On May 7, 2016 Bonomo scored his first goal of the season scoring the game-winning goal in a 3–1 victory over Pittsburgh Riverhounds. On June 26, 2016 Bonomo helped New York to a 4–0 victory against the Wilmington Hammerheads scoring his second goal of the season. On October 23, 2016 Bonomo came on as a second-half substitute and was involved in two late goals to help New York to a 5–1 victory over Swope Park Rangers in the 2016 USL Cup Final.
