A few minutes later two more people were located and bought on board the vessel.
The trio were transferred to NZ Steel Waiuku Rescue for treatment before being taken to a awaiting ambulance.
Waiuku Coastguard and surf lifeguards from Karioitahi and Sunset Beach clubs helped rescue the people from the water, along with the Police Eagle Helicopter.
Winyard said the trio were hypothermic, one severely. One of the boaties also had a cut on their hand. Two were treated by ambulance staff at the scene, while a third person was taken to a local medical centre.
He said the boaties were "pretty lucky" to be found as they did not put in a call to Coastguard or Maritime before crossing the bar - a procedure boaties must follow before crossing a bar.
"We can't stress enough the importance of carrying two forms of communication with you and logging a Bar Crossing Report with Coastguard Radio. If this had been the case our response time would have been significantly reduced, the men are extremely lucky that the member of the public raised the alarm when they did," said Winyard.
"Wearing a lifejacket especially at times of risk such as crossing a bar will save your life."
Surf Life Saving New Zealand spokesman Allan Mundy said the mouth of the Waikato River was a complicated area to navigate. He said there was also a swell in the area at the time the boat capsized.
He said anyone crossing the bar needed to be confident boatie.
The rescue is one of six incidents responded to by Coastguard volunteers around the northern region so far today.
These included a diver who was taken to hospital after he surfaced from a dive near the bottom end of Waiheke Island and started suffering from vomiting and dizziness.
Coastguard Maraetai responded to the call for help and transported the patient quickly to an awaiting ambulance.
