Mayor Bill de Blasio wants to sink a fleet of floating billboards that he says are turning New York’s scenic waterways into a Times Square-style blight.

The city filed suit Wednesday in Manhattan federal court against a company called Ballyhoo Media, which is described on its website as a “water-based multimedia company.” The suit alleges that the LED-illuminated seafaring signs along the Hudson and East rivers create a “public nuisance” that distract motorists and spoil the view for sightseers — and also are breaking local zoning laws.

“Our waterways aren’t Times Square. These floating eye-sores have no place on them,” said de Blasio in a statement about the suit. “Ballyhoo is operating in direct violation of the law, and we are filing this suit to put a stop to it.”

According to the suit, the signs, which have carried advertisements for Heineken and the Universal Pictures film “Dr. Seuss’s The Grinch,” among others, generally follow a route from the Intrepid Sea, Air & Space Museum on the west side of Manhattan south around Battery Park and up to Roosevelt Island or along the Brooklyn shoreline on the East River.

“As detailed in our complaint, Ballyhoo continues to operate its water-based ads in defiance of local laws intended to further traffic safety and promote the various uses of waterfront areas for the public,” said city Corporation Counsel Zachary Carter.

“Ballyhoo openly promotes its large, water-based, LED billboards as specifically designed to attract the attention of drivers, necessarily posing a serious safety hazard on busy waterfront highways. We have asked the Court to impose civil penalties upon Ballyhoo and to order the company to abate its violations in the best interest and safety of the public.”

City attorneys contacted Ballyhoo in January to put the company on notice that the billboard barges violate city zoning laws pertaining to outdoor advertising, the suit states, but the company’s attorney informed the city that it would not stand down.

Adam Shapiro, Ballyhoo’s CEO, issued a statement saying his company spoke with “numerous” law firms before it began operations in New York and that it was determined that the way it does business falls within the bounds of the city’s zoning laws.

“Advertising along the city’s waterways is not new activity, Ballyhoo just happens to be the newest,” the statement reads.

The zoning resolution prohibits the operation of advertising signage in waterways adjacent to any of the three major types of zoning districts in the city — residential, commercial and manufacturing — and within view of any major highway or bridge. According to the company, the boat’s standard route begins on the Hudson River in Midtown, heads southbound around Battery Park, and continues up the East River to Roosevelt Island.

“New York City’s waterways are among our most precious public resources. Decades ago, planners had the foresight to write zoning regulations to prevent advertising on our rivers and harbor, protecting their natural beauty. Just because technology makes these ads more visible, doesn’t make them legal,” said Department of City Planning Director Marisa Lago.