The Seastreak service from the Rockaways to Lower Manhattan began in November of 2012, when the peninsula had no subway service.
The ferry is popular, and the city will continue to subsidize it through next January.
The weekday ferry runs from Beach 108th Street, then stops at the Brooklyn Army Terminal at 58th Street before heading to Pier 11.
Riders can transfer from there to 34th Street.
The one-way fare is $2.
The ferry service has allowed for more than 120,000 passenger trips since its initial launch after Hurricane Sandy in November.
"Ferry service has proven to be a popular and effective mode of transportation for Rockaways and Brooklyn residents," Mayor Michael Bloomberg said. "Extending the service through January will allow riders to continue taking advantage of this quick, enjoyable and sustainable transit option."