The former-Barcelona striker, who also finished runner-up for the MLS Golden Boot with 23 goals, beat off competition from Bradley Wright-Phillips and Sacha Kljestan of crosstown rivals New York Red Bulls.
Toronto FC's Sebastian Giovinco, the 2015 MVP, finished fourth in the running for the award, which is voted on by players, club management and media.
Former Spain striker Villa was a key part of New York City's incredible turnaround as the team claimed a postseason spot after finishing 17th in 2015.
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The first player signed by NYCFC, Villa finished the regular season in tremendous form, scoring six goals in his last four appearances, with the team winning three of those contests en route to clinching a playoff spot.
NYCFC finished the season second in the Eastern Conference with a total of 54 points and a 15-10-9 record.
(Reporting by Steve Keating in Toronto; Editing by Tony Jimenez and Toby Davis)
