In February 1927 he immigrated to the United States of America, settling in Jackson Heights, Queens, New York City. In 1928 he married Margaret Mary Egan, a Tipperary-born research chemist, who had been educated at University College Dublin and University of Geneva. Following the creation of Fianna Fáil and their entry into the Irish Parliament Dáil Éireann, Flannery became affiliated with Sinn Féin, who had voted to retain their abstentionist policy towards the Dáil and their refusal to acknowledge it as the legitimate government of Ireland. Sinn Féin tasked Flannery with drumming up support for the party in New York. However, following the start of the Great Depression Flannery found it difficult to focus on politics in the face of mounting poverty. By 1933 finding support for Sinn Féin and the IRA became particularly tough when Fianna Fáil expanded greatly the range of people eligible for military pensions, which under the previous government had been biased against members of the Anti-Treaty IRA. For the next 40 years Flannery would work for the Metropolitan Life Insurance Company.
During The Troubles
Upon the onset of The Troubles in Northern Ireland, Flannery was once again drawn into the world of Irish Republicanism. In a response to the mounting violence, Flannery set up the Irish Northern Aid Committee, or as it became better known as, NORAID. The official purpose of NORAID was to provide funds to the families of imprisoned Irish Republicans and victims of violence. However, opponents levelled the accusation against the organisation that it was also providing funding directly to the Provisional Irish Republican Army, and perhaps even also supplying firearms. In 1970 he travelled around America and set up 62 chapters of NORAID. In 1971 he said: "The more coffins sent back to Britain, the sooner this will be all over", referring to British soldiers. In 1982 he was indicted, with four other members of NORAID, for arms smuggling, but all defendants were acquitted after their legal defence was able to successfully argue their actions had been sanctioned the CIA. Four months after the verdict of the arms trial, Flannery was named as Grand Marshall of the Saint Patrick's Day Parade in New York City. His appointment caused considerable controversy within the Irish-American community and several high profile figures boycotted the parade that year, including the Archbishop of New YorkTerence Cooke. In 1986 Flannery quietly resigned from NORAID following the decision by Sinn Féin to drop its abstentionist policy in the Republic of Ireland and to recognise Dáil Éireann as the legitimate governing body of Ireland. He opposed the Northern Ireland peace process, believing that Sinn Féin and the Provisionals had "sold out", and believed the removal of British troops from Northern Ireland was the only starting point upon which negotiations could begin. He died 30 September 1994, aged 92.