Mr McIntyre interviewed 26 republicans and also put his own story on record as part of the controversial history project.
But speaking to UTV from his home in the Republic of Ireland, he described it as a "disaster".
He said: "I think the project as constituted with Boston College has been pretty much a disaster but I think that type of project is vital to a much better understanding of society and political conflict."
As the college moved to distance itself from the project, he continued: "I wish Boston College had been prepared to have distanced itself from the tapes three years ago when I and Ed Moloney urged it to either hand them back to me for safe keeping and I would lodge them somewhere else.
I was quite prepared to go to prison and never let the PSNI get access to them or, as Ed Moloney suggested, destroy them – and I supported him on that.
Asked if he thought it would ever get to this stage, he added: "Not at all, otherwise I would have refused to have been involved in it. There was no point in risking the safety of the interviewees, my own safety and the wellbeing of my family by bringing this disaster down round my ears."
Earlier the journalist behind the Boston tapes, Ed Moloney, strongly refuted any suggestion that the controversial history project was designed to target Sinn Féin leader Gerry Adams.
The comments come as it emerged that tapes of interviews with former republican and loyalist paramilitaries could be handed back to those who took part.
The recordings are known to include accounts from high-profile figures like IRA members Brendan Hughes, Ivor Bell and Dolours Price, and UVF man turned PUP leader David Ervine.
According to Mr Moloney, a "concerted attack" has been made on the integrity of the project.
Those involved agreed to give interviews on the condition that the information would not be made public during their lifetime.
Details have since been revealed, including accusations against Gerry Adams - which he was questioned about following his arrest over the 1972 murder of Jean McConville.
He was detained at Antrim PSNI station for four days before being released pending a report to the Public Prosecution Service.
I welcome the end of the Boston Belfast Project, indicated by the College's offer to now return the interviews to the interviewees, before the securocrats who cannot live with the peace seek to seize the rest of the archive and do mischief.
Gerry Adams, Sinn Féin
Mr Adams, who denies any involvement in the disappearance, murder or burial of Jean McConville, has said that the 'Belfast Project' at Boston College was "flawed from the start".
He added: "Everyone has the right to record their history, but not at the expense of the lives of others ... I was not and am not aware of any republican or member of Sinn Féin in support of the peace process who were approached by Anthony McIntyre to be interviewed.
"On the contrary, the individuals so far revealed as having participated are all hostile to Sinn Féin."
But Mr Moloney insists: "There were over 200 interviews from 26 participants housed in the Boston College archive and Mr Adams has not read them, does not know their full content and, aside from two or three names that are in the public domain, does not know who was interviewed.
"He speaks from a position of almost complete ignorance about the archive."
According to Mr Moloney, only one person besides himself and Anthony McIntyre has read the full archive - Judge William Young who presided over the first hearing dealing with the subpoenas.
"Judge Young could find only one interview that was fully responsive - that dealt directly with what had allegedly happened to Jean McConville," he said.
"Another 10 or so interviews made some reference to her ...
"Even if an interviewee had said: 'I don't really know much about Jean McConville other than what I have read in the papers', then that interview had to be surrendered.
"Out of over 180 interviews that he read, only 11 met Judge Young's generous criteria for surrender."
If this was indeed a 'Get Gerry Adams' project, then all I can say is that we did not do a very good job of it.
Historian Eamon Phoenix has told UTV that the return of the Boston tapes and the break-down of the project would be a blow in terms of documenting the history of Northern Ireland.
"This was an attempt to add a new dimension," he said, of efforts to record interviews with key figures involved in the Troubles.
"Yes, we'll have the State papers. Yes, we'll have the memoirs and books written by individuals on the security services or indeed the IRA or loyalist paramilitaries.
"But now you would actually hear the voices. In 100 years' time, when we're talking about the ceasefire of 1994, you would hear the voices of Brendan Hughes and David Ervine from that period.
"It seemed a great idea ... I can see the value of it."
But Mr Phoenix added: "The fact it has been used in an evidential way by the PSNI, for example, has soured the whole idea.
"Certainly, I think interviewees who have a paramilitary past would be very reluctant to commit to take part now."
Most members of the History faculty were unaware of the existence of the project until the publication of Moloney's book Voices from the Grave in 2010.
Boston College has also moved to distance itself from the history project.
A statement notes: "The project was funded by Boston College and is housed in the Burns Library, the special collections library of the university, and portions of it have recently been made available under court order to British authorities."
But it goes on to outline: "The interviews that make up the archive were conducted by former members of the paramilitary organisations, who were hired by the journalist Ed Moloney.
"Neither the interviewers, Anthony McIntyre and Wilson McArthur, nor Mr Moloney were employed in or by the History Department at Boston College.
"They were subcontracted to do the job by people acting outside the department and without the involvement of the department."
The college also claims that "successive department chairs had not been informed of the project, nor had they or the department been consulted on the merits of the effort or the appropriate procedures to be followed in carrying out such a fraught and potentially controversial venture".