The temporary ferry from Great Kills to the East River ended Friday.
The service was launched in November for those living in areas hard hit by Hurricane Sandy.
Passengers paid $2 a trip to go from Great Kills Park to Pier 11 on East 35th Street in Manhattan.
Transportation officials said they decided against extending the eight-week run because the service was underused, with an average of just 114 riders each day.
Staten Island lawmakers said they will explore alternatives for Staten Island commuters.