The Madison County Sheriff's Office says the deaths occurred in the rural town of Smithfield, between Syracuse and Utica, after the storms hit at about 7 p.m. Tuesday.
Officials say Wednesday that at least four homes are completely destroyed and numerous others are damaged. More information is expected to be released at a morning news conference.
About 72,000 homes and businesses are without power, most in central and northern New York.
The National Weather Service says investigators will be in Smithfield to determine if a tornado touched down.