Starting this June, there will be year-round, every day ferry service connecting Fulton Landing, at the foot of Old Fulton Street, and other points in Brooklyn and Queens, with downtown and midtown Manhattan. During the summer this service will be extended to Brooklyn Bridge Park’s Pier 6, near the foot of Atlantic Avenue.
New York Times: For all their dominance on Staten Island, ferries have long struggled to muscle their way into the city’s mass transit mainstream. Experiments in Queens and Brooklyn have been held back by infrequent service, outsize operating costs and low ridership.
Under the plan, to be announced on Wednesday, ferries will travel along a seven-stop route that stretches from Long Island City, Queens, to the Fulton Ferry landing by the Brooklyn Bridge, and includes Manhattan terminals at Pier 11 in the financial district and East 34th Street. During peak hours, boats will arrive at each stop every 20 minutes and travel in both directions.
According to the Times article, the city has committed to subsidize the service for a minimum of three years. The fare between Fulton Ferry or Pier 6 and downtown Manhattan will be $3.00; to or from midtown it will be $5.50. See the linked Times article for a map of the service.