It happened just before 9:30 a.m. at 69th Street and Columbus Avenue.
The 47-year-old victim was shot in the leg and shoulder by another man who fled down 69th Street toward Central Park.
Police believe the suspect ran into the subway at 72nd Street and Central Park West.
Authorities had the power turned off so officers could walk the tracks in case the suspect was hiding in the subway tunnel north of the station.
Some passengers had to be evacuated and A/B/C/D trains were delayed for the investigation. Subway service was restored shortly after 11 a.m.
Investigators now believe the suspect may have left the subway through an emergency exit at 76th Street and they are searching Central Park.
The victim was taken to Mount Sinai Morningside and is said to be stable.
The suspect was last seen wearing a white hat, green jacket, blue underhoodie and holding a black gun in his hand.
West End Secondary School was briefly locked down after the shooting.
The shooting comes one week after two people were shot just blocks away during trick-or-treating hours on Halloween.
The investigation into Thursday morning's shooting is ongoing.
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