On Monday, the sailboat was nearing the US coast with strong downwinds.
"Strong winds are pushing us west. We expect to arrive at North Cove Marina in Manhattan, New York sometime Tuesday afternoon or evening," Ms Thunberg wrote on Twitter.
In a video post published late Sunday, she said the boat was travelling at "between 20 and 25 knots" and it was "very rough, and very high waves."
The teen marked the first anniversary of the start of her school strike on August 20.
She began sitting outside the Swedish parliament in August 2018 to raise the awareness of members of parliament to the urgency of climate change.
She was swiftly joined by other students around the world, as word of her strike spread through the media, and the "Fridays for future" movement was born.
The 18-metre yacht features state-of-the-art solar panels on its deck and sides while there are two hydro-generators which together provide all the electricity needed on board.
Her voyage has however sparked controversy after a spokesman for Herrmann, the yacht's co-skipper, told Berlin newspaper TAZ that several people would fly into New York to help take the yacht back to Europe. Mr Hermann himself will also return by plane, according to the spokesman.
Team Malizia's manager insisted however that the young activist's journey would be climate neutral, as the flights would "be offset."
Ms Thunberg has said that she doesn't yet know how she will return to Europe when the time comes.