New York (8-4-3) has managed only two points from its last three games after winning five in a row. Vancouver (7-3-5) is unbeaten in its last five contests.
Both teams are in third place in their conference.
The game was scoreless until Martin Bonjour took a feed from Alain Rochat in the middle of the penalty area and drove the ball into the top-right corner for the Whitecaps in the 75th minute.
Bonjour's effort was the only shot on goal for Vancouver during the entire game.