Mona Kanciper, of Manorville, on eastern Long Island, also was charged with two counts of endangering the welfare of children.
Officials said she performed the euthanization in front of minors.
Chief Roy Gross of the Suffolk County SPCA did not identify the children or their relationship to the woman.
Gross said his investigation began in December 2009.
Officials initially looked into allegations that horses had been improperly euthanized. Gross said there was no evidence to support that.
Neighbors of the Butler Farm and know the owner Mona Kanciper, say there's just no way the woman who dedicated her life to rescuing horses would torture an animals.
"She botched the job had to strangle the dogs after it didn't work," said Gross.
Police executed search warrants and found remains of dogs, horses and drugs and syringes used to euthanize animals.
Heather Petrie is a caretaker of horses and says there's no excuse or explanation. "Take it to a vet, you don't do that," she said.
Kanciper founded New York Horse Rescue with her husband, Judson Butler, a well known vet who died of complications last year.
Online: New York Horse Rescue