Activists mainly from the Coalition to end US Saudi Alliance movement staged a rally near Wall Street, as Mohammad bin Salman was expected to hold a score of business meetings, as well as meeting with UN Secretary-General Antonio Guterres.
Saudi Arabia's Crown Prince Mohammed bin Salman arrived in the United States last week for a multicity trip.
The trip is Crown Prince Mohammed bin Salman's first since replacing his cousin as Saudi Arabia's king in waiting last year. It also follows his controversial arrest of hundreds of wealthy Saudis, including princes, officials and businessmen in November.
Although the Trump administration staged a warm welcome for Saudi Crown Prince, he faces different protests in US mostly organised by antiwar activists.
The two-week long visit by Mohammed bin Salman to the US is is also being overshadowed by an ongoing legal battle being waged by the families of hundreds of people killed in the 9/11 attacks.
Nearly 3,000 people died when hijacked airplanes crashed into New York's World Trade Centre, the Pentagon building and a Pennsylvania field in September 2001. lawyers for the families of the victims launched a string of compensation claims against Saudi Arabia in 2016, alleging Riyadh channelled money to support the attacks.