NY Waterway offers excursion and sightseeing trips[5] to Yankee Stadium,[6] Gateway National Recreation Area, and Governors Island.

In 1986, Imperatore established New York Waterway,[8] with a route across the river between Weehawken Port Imperial and Pier 78 on the West Side of Midtown Manhattan.

[11] NY Waterway briefly also operated a high-speed ferry from Staten Island to East 34th Street in 1998,[12] but discontinued it due to low ridership.

[13] The September 11, 2001 attacks on the World Trade Center destroyed the PATH terminal located there, greatly reducing cross-Hudson River passenger capacity.

The company was well-positioned to take advantage of government investment in ferry service, receiving subsidies and generous agreements to docking at public facilities.

[11][14] NY Waterway service quickly expanded by adding new routes and increasing the frequency of crossings, heavily borrowing to fund the acquisition of additional vessels.

After PATH service was restored ridership significantly declined, the loss of passengers brought the company, unable to reduce its fixed costs, to brink of bankruptcy.

[26] In the immediate aftermath of collapse of the World Trade Center, the company played a major role in the maritime response following the September 11 attacks and the evacuation of passengers who otherwise would have been stranded[27] because of the chaos in the regional transportation network.

In January 2009, the company was instrumental in the rescue of passengers of US Airways Flight 1549, which made an emergency landing on the Hudson River after both of its engines failed.

NY Waterway sold the upland property and in November 2017 purchased the former Union Dry Dock 8-acre (3.2 ha) site in Hoboken to build a new facility.

[36] NY Waterway and city reached a deal in which the ferry company would sell the land to the municipality for about $18.5 million, but the sale as of November 2022 had not been finalized.

[42] On November 24, 2019, the U.S. Coast Guard pulled 23 ferries out of the company's 32-vessel fleet due to safety issues following a routine annual inspection.

[45] In June 2012, New Jersey Transit and NY Waterway began a fare-sharing program for riders transferring between the Hudson-Bergen Light Rail and ferries at Port Imperial for ten-trip and monthly tickets.

[50] In January 2016, NY Waterway and NJT introduced the Hudson GoPass, allowing for unlimited use on light rail, ferry and bus routes 156, 158, 159.

At various points in the past, NY Waterway has also provided ferry service to other destinations including LaGuardia Airport, Newport, Harborside, Liberty State Park, Belford, Sandy Hook, and Belmar, New Jersey.