Sandra Sharma, 42, and her daughter Marie Sharma, 27, were both charged in Staten Island Criminal Court. Sharma's 21-year-old son, Thomas Therrien, who also worked at the New Beginning store, was charged with conspiracy to commit arson.
All pleaded not guilty.
Cops said the women had provided a videotaped confession in which the elder Sharma admitted she "hatched a plot to use fire to do away with the clothing." They said she had talked her daughter into setting the blaze Tuesday at the store, at 225 Broad St. in Stapleton.
"I was sick of folding clothes," she allegedly told police.
Officials said store owner Christopher Fabanwo, 50, had kept piles of secondhand clothes in the rear of his store, and died trying to salvage his property more than a year after another thrift store he had owned burned down.
They said Fabanwo, a Nigerian immigrant, rushed into the burning store, pulled his employees to safety, and ran back with a fire extinguisher. He was overcome by smoke, went into cardiac arrest, and died later at Staten Island Hospital.
Nearly 200 firefighters fought the blaze for three hours, and eight people were slightly hurt.
Fabanwo's 48-year old widow, Temitayo, told The Post she tried to break down a door to rescue her husband, but it was too late.
Fabanwo said she and her husband, who arrived in the United States 15 years ago, had four children, ages 15 to 26. She said she had an "excellent relationship" with the accused.
Fabanwo said she and her husband had opened A New Beginning after the previous store burned down.
"We came looking for a bright future, but our American dream is gone now," she said. "We lost it all in the first fire, then we refinanced our house and started over. I've lost everything. My husband, my store. But I have God. God will see me through."
The Sharmas were held without bail. Therrien was held on $50,000 bail. All three were scheduled to appear in court tomorrow.
Mark Fonte, a lawyer for the elder Sharma, said his client had no reason to kill Fabanwo.
"She is mourning the loss of her friend," he said.