"No Trump, no KKK, no fascist United States of America!" protesters chanted while holding signs with slogans including "White Supremacy is Terrorism".
President Trump has a large, inflatable surprise waiting for him when he returns to Manhattan - a giant rat made in his likeness.
No protesters could be seen from the motorcade along the way, as many were gathered on a different street from the motorcade's route.
Mayor Bill de Blasio said Trump is set to be in NY from Monday to Wednesday, but noted that the schedule was subject to change.
As the NYPD began shutting down streets hours before President Trump arrived in Manhattan Monday, New Yorkers couldn't hide their annoyance.
Trump was supposed to arrive to NY on Sunday, but the trip had to be delayed.
Trump, who is now on what he has called a "working vacation", is due to spend two nights in his Trump Tower apartment.
His response to the violence in Charlottesville was criticized by some on both the left and right who said he needed to condemn white supremacists and place the blame on far right groups for sparking the violence.
Other protesters held aloft signs that read "Too little".
She lifted the words from a speech then-candidate Trump gave on the campaign trail, where he was referring to calling out Islamic terrorism.
Teacher Kevin Gallagher, 61, said he at first gave Trump "a chance" despite his dislike of the Republican.
"He knows it's his base, and he doesn't want to alienate it".
As the weekend continued, the White House faced even more questions about why Trump seems strangely hesitant to denounce his racist supporters (some of whom were present in Charlottesville).
Blasio condemned the violence over the weekend, saying: "This white supremacist movement is a danger to us all, including our law enforcement officers who often engage with these hate groups. It took until today to say the words KKK, neo-Nazi".
President Trump admits his upcoming visit to New York City will be "very disruptive".
Just before 6:30 p.m. on Monday, the president wrote on Twitter that he was heading to New York City.