Jean McConville was taken from her home in Divis Flats in Belfast in 1972.
She was murdered and secretly buried on a beach in County Louth by the IRA.
Her son Billy told the Historical Institutional Abuse Inquiry he was abused by some De La Salle Brothers and physically abused by a lay teacher in Rubane House in County Down.
He said: "It was one hell of a nightmare".
He also said he believed there was "a conspiracy between the RUC and De La Salle Brothers" over what was happening at Rubane at the time.
Mr McConville, who is now 48, claimed he was also abused at Rubane House by the notorious paedophile priest Fr Brendan Smyth.
He told the BBC that he also blames the IRA for the abuse he claims he suffered.
Two other witnesses also made allegations of physical abuse against the same lay teacher named by Mr McConville.
One claimed he was "kicked and punched" while another said he suffered "a black eye and a burst nose".
However, in a statement read to the inquiry, the former teacher said he always carried out his duties with "care and compassion".
He described the allegations against him as "complete fiction" and "totally ridiculous".
The son of an IRA murder victim has claimed he suffered sexual and physical abuse in care.