More than 400 voters were queued up outside Madison Square Garden an hour before doors opened at 10 a.m. By mid afternoon, the NYPD said 5,000 people were on line.
Blocks-long lines were reported outside the Barclays Center in Brooklyn, and in Harlem, Astoria, Bayside and Williamsburg.
New York, which began offering early voting only last year, is among the last states to start the process for this election. Maryland will begin early voting Monday and the District of Columbia Tuesday.
A total of 93,830 New Yorkers voted Saturday: 29,411 in Brooklyn; 19,877 in Manhattan; 19,223 in Queens; 14,928 in the Bronx; and 10,391 on Staten Island, according to the Board of Elections.
So far, at least 56 million Americans have voted, either in person or by mail, according to The Washington Post. The number doesn't include NY ballots and is already 119% of those who voted early in 2016 with 10 days to go before Election Day.
In Florida, more than 5.2 million people have voted already, a number that exceeds the 4.61 million who voted for Trump in 2016, according to a Newsweek report.
Many New Yorkers said they were voting early because they feared fraud or didn't trust the post office to handle absentee ballots.
Actor Timothee Chalamet was among the throngs at the Garden, emerging shortly before 4 p.m. wearing a baseball cap and blue mask.
"I'm here because I'm trying to take part, like everybody else, in saving this democracy," he said after posing for photos with fans. "Everybody vote! Everybody vote!"