On Sunday, Thunberg had said on Twitter that the vessel, the Malizia II, was due to dock in the city on Tuesday.
But in an update late on Monday, she said that weather would delay its arrival.
“Day 13. Rough seas south of Nova Scotia,” wrote Thunberg in a tweet.
“But conditions closer to New York will be slower than predicted and weather update suggests Wednesday arrival – an updated ETA will come as we near the coast.”
Thunberg is on her way to speak at the UN Climate Action Summit on September 23, and is traveling on a zero-emissions sailboat to reduce the environmental impact of her journey, according to a statement from her team.
The Swedish 16-year-old has become the figurehead of a burgeoning movement of youth climate activists after her weekly protests inspired student strikes in more than 100 cities worldwide. UN Secretary-General António Guterres has called on world leaders to present concrete plans to reduce greenhouse gas emissions at the upcoming summit.
“The estimated arrival time is tomorrow Wednesday or on Thursday, it still depends on the wind a bit,” a member of her team told AFP on Tuesday.
Thunberg set off from Plymouth, UK on board the Malizia II yacht on August 14.
The boat is captained by Boris Herrmann, a professional race skipper, and Pierre Casiraghi, founder of the Malizia team.
The Malizia II will allow her to make a zero-emissions journey thanks to solar panels and underwater turbines that generate electricity.