The ride, which costs $3.50 each way and runs from Rockaway Beach to Manhattan with a stop in Brooklyn, was introduced after the hurricane as a transportation option since the A train was knocked out of service.
The ferry was allotted $2 million in the budget to fund it through October, according to the Economic Development Corporation.
But beyond that, the future is fuzzy.
Queens Borough President Melinda Katz, along with the city's four other borough presidents, sent a letter of support for the ferry to Mayor Bill de Blasio, requesting he include $8 million in his budget to allow the ferry to sail seven days a week through June 2015.
“In the short time since it was established during the immediate aftermath of [Hurricane Sandy], the temporary Rockaway ferry has proved enormously popular and has contributed to the peninsula’s economic growth and to its attractiveness as a tourist destination," Katz said.
The long-term funding was not added as the city continues to "examine ridership and seek a sustainable funding stream that can support the $25 to $30 subsidy per trip — the highest by far of any public transportation in the city," according to EDC spokeswoman Kate Blumm.
Other politicians, including state Sen. Joseph Addabbo, Jr., vowed to continue their fight to make the boat ride permanent. Addabbo said he believed the city could "find the fractional money needed to keep the ferry afloat permanently" in its $75 billion budget.
The ferry has been viewed as an integral part of the peninsula's recovery from the hurricane, offering an alternative to the A train and buses.
The EDC's president, Kyle Kimball, even told a group of real estate developers at a symposium in March that the Rockaway peninsula would be the city's next breakout neighborhood, according to a report in The Real Deal.
“We’re astounded by what we’re seeing there,” Kimball said.
Assemblyman Phil Goldfeder said he was "severely disappointed" by de Blasio and the EDC for "ignoring the transit needs of southern Queens and Rockaway families," especially given its view as a burgeoning community by the EDC.
"The city needs to put its money where its mouth is," he said.