Steven Eldridge, 42, of Penn Yan, was arraigned on five counts of criminally negligent homicide, driving while intoxicated, reckless driving, unsafe passing, speed not reasonable and prudent, and failure to keep right after passing.
Eldridge was held on $250,000 cash bail or $125,000 bond, the newspaper said. His next court date is Friday. It was not immediately clear if he had a lawyer.
Yates County Sheriff Ronald Spike said five people in the van were pronounced dead at the scene of the 12:40 p.m. crash. Nine others, including the tractor driver, were taken to area hospitals, many of them with extensive injuries. One person was treated at the scene and the car's driver suffered minor injuries but was not hospitalized.
There were 14 people in the van; the driver was not Amish, as they generally don't drive.
The Sheriff's Office identified the victims late Tuesday as Melvin Hershberger, 42; Sarah Miller, 47; Melvin Hostetler, 40; Anna Mary Byler, 60; and Elizabeth Mast, 46.
"In passing, (the car) glanced off the van and went off the highway and the van ended up going underneath the farm tractor," Spike said. The car tried to go around the tractor in a no-passing zone near where the 55-mph stretch of two-lane blacktop curves and signs recommend reducing speed to 45 mph.
"It's just a horrific tragedy," Spike said. "It really strained the EMS services and fire departments. There was a lot of hard work at the scene."
The task of identifying the dead and injured was made difficult because many Amish do not carry identification, Spike said. One of the survivors was able to give them some information at the scene and a group of Amish residents from the Jasper-Woodhull area helped identify a female victim at a hospital.
Spike said the victims were all from Steuben County. The group was visiting other farms in New York's rural Finger Lakes region on an excursion organized by Cornell University to learn techniques compatible with their religion. Spike said authorities initially thought the farmers were Mennonites.
New York has seen a boomlet in new Amish colonies recently, driven by affordable rural farmland and proximity to traditional population centers. A study by researchers at Elizabethtown College in Pennsylvania found the Amish have established 10 new settlements in New York since the start of 2010. Total population has grown by more than a third in the past two years, to 13,000.
The tractor was carrying a large spraying implement. At least four people were stuck in the wreckage before they were removed by emergency responders who used power cutting tools to free them.
Four hours after the crash, responders were still removing pieces of the van from under the tractor and loading it on a flatbed truck.
"It took a long time to get the individuals out because the van ended up entangled and underneath the large tractor with the spray equipment on it," Spike said.
"It's probably one of the worst accidents we've had in this county that I can remember," he said.
The crash happened 43 miles southeast of Rochester and about 30 miles northeast of the spot in Steuben County where a tour bus crashed Sunday on Interstate 390, killing two people and injuring 35. It's a mostly agricultural swath of land, and the road where Tuesday's accident happened carves its way between large soybean fields.
A dispatcher said four helicopters, several fire departments and about a dozen ambulances services were called to the scene. Seven of the injured were taken to Strong Hospital and two went to Geneva General Hospital.
Tim Raths contributed to this report from Washington, D.C., and Mary Esch contributed from Albany.