The first commuter ferry, the 'Urban Journey', took off from the new Rockaway route at 5:30 a.m. and then picked up more passengers at Sunset Park before arriving in Lower Manhattan.
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More than 100 people were on board for the pre-dawn launch.
Riders from the Rockaways will be able to get to Manhattan in just about an hour. A one-way ride costs $2.75.
The Rockaway Route offers service between Beach 108th Street, the Brooklyn Army Terminal, and Wall Street's Pier 11.
The ferry will service Manhattan, Brooklyn and Queens.
Renovated ferries also launched Monday on the existing East River route.
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Mayor De Blasio took the ceremonial first ride Sunday, traveling from the Rockaways to lower Manhattan.
The city is making a $335 million bet that the service will attract millions of passengers traveling between Manhattan and waterfront neighborhoods in Brooklyn, Queens and the Bronx that are now a distant walk from overcrowded subways.
It is the first permanent ferry service for the Rockaways. There was a temporary ferry following Superstorm Sandy but that ended in 2014.
The mayor says this will be a lifeline for many.
"They've been isolated for a long time, literally decades, they haven't had enough opportunity, haven't had enough access to what the rest of the city has to offer," said de Blasio.
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By June 1st, the city hopes to have the South Brooklyn route up and running, in August, Astoria and by next summer the Soundview and Lower East Side routes.
"This is a milestone two years in the making. New ferries are crisscrossing out waterways, opening up more opportunity for New Yorkers and businesses. NYC Ferry has officially launched, and we look forward to expanding the system to reach even more neighborhoods," said Deputy Mayor for Housing and Economic Development, Alicia Glen.
The ferry can carry up to 149 people, and it is WiFi ready along with bathrooms, bike racks, and a snack bar stocked with beer and wine.
Mayor de Blasio personally greeted commuters as they arrived in Lower Manhattan. They in turn told him, thank you and job well done.
Together they hope it's the beginning of something great, making travel across the New York Harbor a breeze.