NYC ferry is operated by contractors, not the city. Only the SI Ferry is city operated. They are heavily subsidized, it costs way more per ride than the fare.
The NYC Ferry is owned by the New York City Economic Development Corporation and is run by the contractor Hornblower. Mayor Bill De Blasio was heavily involved. He is also against the previous air train proposal and I think this would be a solution that would make sense.
The subsidies of the system are already in place and no additional significant subsidizes would be needed. The airtrain proposal was 2.1 Billion dollars. You could easily raise fare prices on the La Guardia ferry route and other routes in the system. Much cheaper cost to provide direct access to Manhattan and other parts including the Astoria Queens ferry stop and more.
i disagree with De Blasio on the subsidizes already in place but I would not dismantle the ferry system and I don’t believe it will be. Fares can be raised and routes adjusted but the link to La Guardia airport using the NYC ferry seems like the best option and is much better than a train or direct subway solution. Better transit links can be improved on the NYC ferry side in Manhattan for instance such as the second avenue subway project which runs close to some ferry terminals and a very small extension could be done specifically for the NYC Ferry terminal with pedestrian walkways underground to the 2nd avenue subway stations or other likeminded solutions. There are definitely solutions doable for a much lower cost using the existing NYC Ferry already in place.
Considering usage patterns of the NYC Ferry which was heavily utilized prepandemic, it seems more than likely this solution will be used by those looking to get to the airport and will avoid traffic jams as well. Woule transit times to get into Manhattan be quicker than going out of the way to willets point and using the LIRR Port Washington Line or overcrowded 7 Subway line?
Another ferry terminal may be needed and the only line that goes by close is the Hells Gate area where there are no rail stations. Manhattan does add some time to the ride. All are welcome to comment. Ferry solution is doable but also seems to have some barriers. Ferry seems somewhat better snd cheaper than rail based solutions if something can be worked out.
Closest space between Ferry and subway station seems to be at Roosevelt Island with an F connection, The ferry is on the opposite side and a little further away, Perhaps Roosevelt Island could have the boats directly to La Guardia Airport snd they can rework it so the ferry and subway statio are better integrated,