Capt Mark Duffy died when the Rescue 116 aircraft crashed about 13km off the County Mayo coast on 14 March.
His body was found last Friday inside the helicopter, which lies about 40m underwater in the Atlantic Ocean.
He was one of four crew members on board when the helicopter crashed.
A lone piper led the Capt Duffy's funeral cortege to St Oliver Plunkett Church in Blackrock, County Louth on Thursday, where a service, attended by Irish President Michael D Higgins, was held.
His coffin was followed by his wife Hermione and their children Esme and Fionn.
Capt Duffy's uncle, Father Stephen Duffy, led the service, and told mourners he had lost his "best friend", who was "one of God's finest creatures".
He added that his nephew had been proud to serve as a pilot and his "first thoughts were always for his children".
"Indeed, he had other attributes which singled him out - a vivacity, a tremendous sense of fun."
Fr Duffy said the crash and loss of the crew was "more than a family grief - it is a community catastrophe".
Uniformed officers and colleagues from the Irish Coast Guard and other rescue services guarded the coffin as it was carried indoors.
The body of only one of Capt Duffy's other colleagues - Capt Dara Fitzpatrick - has been recovered from the sea.
Capt Fitzpatrick's funeral was held in County Dublin almost two weeks ago.
Searches are continuing for the other crew members, winchman CiarÃ¡n Smith and winch operator Paul Ormsby.
An Irish Coast Guard captain who died in a helicopter crash during a rescue mission had "a desire in all things to help and be of service", mourners at his funeral have heard.