With such a common name it is hard to know the facts of this man's life for certain. What follows is the most likely scenario.
Stephen was born in Scoharie, New York. He might have first lived in Lenox, Massachusetts, where he is recorded in the 1810 census as being the head of household of six "all other free persons." It is possible that his wife died and he later married Margaret (or Mary Ann) Grey, who was White. She might have immigrated from Ireland to Kinderhook, New York. By the birth of his daughter Matilda in 1816, he was living in Whately, Massachusetts. According to the 1820 federal census the Thompsons had moved to nearby Hatfield. The record shows that the household had one "Free White Female" aged 16-25 (Margaret) and the other family members were listed as being "free colored." This includes two boys and four girls under the age of 14, and one male and one female each aged 26-44. Stephen would have been about 54 years old so either the census taker mis-judged his age or he might have been absent the day the census was taken. It is possible that this was a combined household and the male and female between the ages of 26 and 44 were a couple related to Stephen or Margaret. If so, the six children could have been divided between the two couples, with Matilda, at least, belonging to Stephen and Margaret. Julia Ann was born in Hatfield in 1826, John in 1829, and Elizabeth in 1832. By the 1840 census the family was in Hadley, Massachusetts, where Georgiana was born in 1844. In 1850 they were in nearby Amherst and Julia and her husband Dudley Till were living in the household as well.
Interestingly, except for the 1820 census, later reports claim that all people in Stephen's household were "free colored persons." It might be that the census takers spoke to one of these family members and did not see Margaret, but assumed she would be Black as well, since the rest of the family was.
Stephen died of consumption in Amherst on December 18, 1851. He was 85 years old.
Sources Consulted
Black Families in Hampden County, Massachusetts 1650-1865, Joseph Carvalho III, 2011, pp. 45, 141-142, 222, 234