arbee

So far as I'm aware, MTA operates no ferries; nor -- so far as I'm aware -- does it or NY State subsidize any ferries operating in NYC waterways. (NY Waterway operates a ferry between Ossining and Haverstraw; also, connecting Newburgh and Beacon. Dunno whether either of these receives any MTA / NY State subsidy. Proof is left to the student; it's irrelevant to this thread.)

NYC's DOT owns and operates the Staten Island Ferry. (The Governors Island ferry is operated by the Trust for Governors Island.) Other ferries operating in NYC's waterways are private; all of 'em. Some -- under the name "NYC Ferry" -- are operated by Hornblower Co. NYC Ferry is subsidized -- deeply -- by NYC's government -- but not NY State's.

For better or worse, when Citibike originated under Bloomberg's mayoralty, it was established as privately-owned and unsubsidized. If they'd asked me (Right; now you tell one....), I might have suggested a different arrangement, but privately-owned and unsubsidized is what we've got. And there are contracts underpinning this arrangement.