The alleged robbers confronted the victim, 24, about 3:30 a.m., flashed a gun and demanded cash, police said.
Two of the men then allegedly held the victim down as a third shot him with the Taser and snatched an undetermined amount of money. The three then fled the train at the 231st Street-Broadway station in Kingsbridge.
The victim declined medical attention.
The alleged crooks were described as 18 to 24 years old and between 5-feet-8-inches and 6-feet tell. All three had medium builds.
Anyone with information about the incident is asked to call the NYPD Crime Stoppers hotline at 800-577-TIPS (8477).