I've recently found that my gr-great grandmother was Kate Diffley, married to John Rooney. I found this on the death certificate of their son, John in 1917. John lived in Paterson and Jersey City with his family. Is it possible that Kate was the sister of your Patrick and John? Do you know birth dates for Patrick & John?
So far, I cannot find any records of Kate Diffley Rooney and her husband in US Censuses. It is possible that Kate stayed in Ireland with her husband John, while other members of the Diffley family emmigrated from Ireland. Do you know if Patrick & John had a sister, or when they immigrated to the US??