The Spanish World Cup winner's goals helped take New York, who finished 17th in their inaugural season, to the club's first appearance in the playoffs.
Villa, 35, scored 23 goals - the second highest tally in the league - and contributed four assists.
The former Barcelona star has been the highest scorer in the MLS over the past two seasons along with Bradley Wright-Phillips, with a combined total of 41 goals.
New York Red Bulls forward Wright-Phillips finished second in the voting for the MLS MVP award, with Sacha Kljestan in third place and Italy's Sebastian Giovinco fourth.