According to
http://www.jfklibrary.org, these are the churches John F. Kennedy visited during his lifetime:
M*achusetts:St. Aidan's Catholic Church - John Kennedy was baptized here in June of 1917
St. Stephen's Church - John F. Kennedy attended often as a youth
St. Francis Xavier - attended throughout his life
Florida: St. Ann's Catholic Church
St. Edward's Catholic Church
New York: St. Joseph's Roman Catholic Church - attended while he lived in Bronxville
Rhode Island: St. Mary's Church - John Kennedy and Jacqueline Kennedy were married here in 1953
Virginia: St. John's Parish at the Middleburg Community Center Building
Washington, D.C.: (attended several during Senate career and Presidency)
Holy Trinity Roman Catholic Church
St. Stephen's Martyr Roman Catholic Church
St. Matthew's Cathedral - *neral was here also