Cardinal Timothy Dolan has also compared IS to the IRA, in that both groups are perverting their religion.
Mr Dolan also highlighted that moderate Muslims are "beginning" to make it clear that Islam does not represent them, and called for them to continue doing so.
He said in an American television interview this week that Islamic State is committing a "... systematic, well-choreographed, very well-focussed attempt to eradicate the ancient Christian population of the Mid-East.
"Remember 30, 35, 40 years ago with the IRA in Ireland? The IRA claimed to be Catholic, OK? And they were baptized; they had a Catholic identity.
"What they were doing was a perversion of everything the church stood for.
He went on to say that "... temperate, moderate, genuine forces of Islam to rise up and say: 'They do not represent us.' Now that's beginning to happen," and that IS is a "particularly perverted form of Islam."