The men, aged 32 and 34, were arrested on suspicion of two counts of attempted murder.
Masked men entered 58-year-old Gerald Deehan’s home on Margaret Street on Tuesday night.
Shots were fired at Mr Deehan and his son Ryan, 30, who has since undergone surgery after being injured in the foot.
Both suspects are in custody at Strand Road police station assisting detectives with their enquiries.
Enquiries into the incident are ongoing.
Anyone with information is asked to contact detectives at Strand Road on 101 quoting reference number 1838 08/10/19.
Information can also be given anonymously through the independent charity Crimestoppers on 0800 555 111.