The animal was first spotted roaming the streets of Harlem late Saturday night.
It headed south, and police picked up the trail in Midtown.
Eventually, officers cornered the critter on Pier 59 in Chelsea at 8 a.m. Sunday.
The coyote was shot with a tranquilizer and taken to a Brooklyn shelter.
Animal Care Centers of NYC in Brooklyn said the coyote is back in the wild in a more "appropriate habitat."