He was taken into police custody following a traffic stop on I-787 Wednesday.
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Nauman Hussain, son of owner Shahad Hussain, handled day-to-day operations for his father, who was out of the country.
As Hussain awaited arraignment and police planned a news briefing on the case, Lee Kindlon, the company's lawyer, said the 28-year-old just handled marketing duties and phone calls while his father ran the company, though police call Hussain its operator.
"My client is not guilty," Kindlon told reporters gathered outside a state police headquarters in Latham. "The police jumped the gun in charging him with any crime."
Hussain has had a brush with law enforcement before. State police accused him and his brother of claiming each other's names after a 2014 traffic stop, which happened while the brother was driving without a valid license.
Saturday's limo crash in rural Schoharie killed 20 people. Two of the victims were pedestrians and the other 18 were headed to a party.
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Relatives said the limousine was carrying four sisters and their friends to a 30th birthday celebration for the youngest.
Autopsies were being performed; authorities didn't say whether the limo occupants were wearing seat belts or give the speed of the limo.
The 2001 Ford Excursion limousine was traveling southwest on Route 30 in Schoharie, about 170 miles north of New York City, when it failed to stop at a T-junction with state Route 30A, state police said. It went across the road and hit an unoccupied SUV parked at the Apple Barrel Country Store and two pedestrians.
The crash appeared to be the deadliest land-vehicle accident in the U.S. since a bus ferrying nursing home patients away from Hurricane Rita caught fire in Texas in 2005, killing 23.
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And it is the deadliest transportation accident overall since February 2009, when a plane crash near Buffalo, New York, killed 50 people, said Robert Sumwalt, chairman of the National Transportation Safety Board, which is investigating.
State officials say the limo involved in the wreck failed an inspection last month and shouldn't have been on the road.
The limo company had said problems with the vehicle had been corrected.
The Associated Press contributed to this report.