NYCFC ended its four-game undefeated streak in the series.
Hines-Ike scored in the 39th minute with an assist from Júnior Moreno.
Canouse scored five minutes later on an assist from Julian Gressel.
Valentin Castellanos scored in the 15th minute for NYCFC.
The Cityzens return to Yankee Stadium for their home opener on April 24 against FC Cincinnati.