The report, exclusively obtained by UTV, says John Martin, Brian and Anthony Reavey were entirely innocent victims.
The three Catholic brothers were shot dead by six masked men who burst into their home in Whitecross in January 1976.
Another brother, Eugene Reavey, battled for decades to clear his name after he was wrongly accused of masterminding the killings of ten Protestant workmen in an IRA ambush 24 hours later.
In 1999 former DUP leader Ian Paisley Sr used parliamentary privilege to accuse Eugene Reavey of masterminding the Kingsmills massacre, one of the worst sectarian killings of the Troubles.
But the Historical Enquiries Team investigation has now completely exonerated the entire Reavey family.
In its final report, the HET says: "There is no doubt that John Martin, Brian and Anthony Reavey were entirely innocent victims.
"Research by HET confirms that they did not have any criminal convictions or links to any paramilitary group.
"No member of the Reavey family had any verified links to any paramilitary group, contrary to later speculation."
Eugene Reavey told UTV it has been an incredibly difficult experience for their family.
"It's not very nice having people turning their back on you walking away from you whispering behind your back."
"I always believed they were innocent. It was a matter of staying with the HET and working with them and finally this is the endgame for us really."
Eugene was in Kingsmills at the time of the attack, but he was on his way to the morgue to pick up the bodies of his brothers.
The security forces had locked down the area and Eugene tried to clear traffic, so he could get to the morgue.
"I was not there for any sinister reason. I was there because I was on my way," he told UTV.
In 2007, the Reavey family received an apology from the Historical Enquiries Team for their treatment by members of the security forces.
Eugene Reavey says he now wants an apology from Ian Paisley Sr for the comments he made in 1999, and is also seeking an apology by the new justice minister David Ford through the assembly.
Eugene Reavey has called for Dr Paisley "to do the decent thing".
"I know he was fed a bum steer when he was given the document but it's not too late for him to apologise to my mother. Forget about me and everyone else I just want him to apologise to my mother," he told UTV.
Those responsible for his brothers' murders are known as the Glenanne Gang, a group which allegedly got help from elements within the security forces.
UTV understands the innocence of the Reavey family was known by police from the start.
According to the HET report, the officer in charge of the investigation said: "No way were the Reaveys involved in any paramilitary activities whatsoever."
He said there was much disinformation, speculative and fabricated intelligence about which hindered investigations.
Four guns were used in the Reavey brothers' killings.
UTV can also reveal that some of these weapons were also used in ten murders, including the killing of three men at Donnelly's bar in Silverbridge in 1975, and numerous other attacks.
No-one has been brought to justice for the murders of the Reavey brothers.
Mr Paisley could not be reached for comment.