A Manhattan federal judge torpedoed a lawsuit filed by New York City targeting floating digital billboards, in the wake of a decision by Gov. Andrew Cuomo outlawing the maritime eyesores — but the company will still have to fork over a $100,000 penalty.

The city originally sued the company behind the billboards, Ballyhoo Media, back in March, claiming the LED-lit seafaring signs sailing along the East River and the Hudson created a “public nuisance” while also breaking zoning laws.

Yet Judge Louis Stanton dismissed the suit late Monday following an agreement between the city and the advertising company, which agreed to hand over a $100,000 judgment to the city as part of the adjudication.

Ballyhoo also promised not to operate the garish advertisements within 1,500 feet of the city’s shoreline, and per court papers, intends to relocate the offending vessel to somewhere in Florida.

Cuomo on Aug. 20 signed into law legislation barring companies like Ballyhoo from operating in New York’s waterways.