The tower was built in the 1970s by a foundation of Iran's former shah
US prosecutors have begun legal action to seize four mosques and a New York city skyscraper that are owned by a non-profit Muslim organisation.
Lawyers say the Alavi Foundation has been helping to illegally funnel money to Bank Melli, which is owned by the Iranian government.
The bank is accused of funding Iran's nuclear weapons programme. US citizens are banned from dealing with it.
The mosques and the office tower will remain open while the case continues.
The government's forfeiture action was filed in a federal court in New York.
Any seizure has to be authorised by the court, and it may take a long time for the case to come to fruition, says the BBC's Adam Brookes in Washington.
Prosecutors are seeking more than $500m (£300m) in assets belonging to the Alavi Foundation, in what could prove to be one of the biggest counter-terrorism seizures in US history.
They include four Shia mosques in New York City, Maryland, California and Houston, as well as a 36-story office building on New York's Fifth Avenue.
The Alavi Foundation owns a 60% stake in the tower, also known as the Piaget building, the Dow Jones news service reports.
Last December, the government filed suit against Assa Corporation, which owns the other 40% stake in the building, and which is also accused of being under Iranian government control.
In court papers filed last month, Assa asked for the case to be dismissed, saying US prosecutors were attempting to "broaden the scope of the US forfeiture laws beyond Congress' intent", Dow Jones said.
Also on Thursday, US President Barack Obama renewed the longstanding US economic sanctions against Iran for another year, the White House said.
Mr Obama sought to reach out diplomatically to Iran soon after taking power in January, but little progress has been made over Iran's disputed nuclear programme.