I don't know about NY Waterway, but many ferry and tour boat operators, along with the big ships, use the UHF "on board" crew HT frequencies in the 457 and 467 MHz band as mentioned for the Staten Island Ferry.
You won't find specific frequencies in the FCC database. The Ship Station License grants authority to use any of the available frequencies.
A list is available on the n2nov website: NYC MARITIME RESOURCES
The Governors Island service is seasonal so there probably won't be anything to monitor until May.
The Trust for Governors Island - Visit the Island