It was Ferris who emerged as the main threat on Sunday, leading home Cooper in race one before Cooper turned the tables on his rival to restore a five point separation with one race remaining.
The crucial point of the day came in race two when Ferris carried superior speed through the tricky sawdust section and grabbed the lead from Cooper. A determined fightback saw Cooper regain the lead within half a lap and secure the win.
"I really had to win that one to have a good chance. So I dug deep and went for it," said Cooper.
In race three the pair made contact in the first corner. It cost Cooper a few seconds before settling into second place and he made sure of the title win by following Ferris to flag and with a two-point advantage.
Three third placings on Sunday confirmed Waters in third place ahead of Queenstown's Scott Columb (Kawasaki) and Taupo's Brad Groombridge (Suzuki).
In a change from recent years Cooper isn't gearing up to take his New Zealand number one status across the Tasman to contest the Australian Nationals which begin next month.
"I have reached the stage where I want to do the races that are fun," says Cooper.
"It's not definite yet but I'm hoping to go to America and ride the opening two rounds of the AMA Nationals."
Those races are in late-May at Hangtown (Sacramento) and Glen Helen (San Bernadino).
Takaka's Hamish Harwood (KTM) won his first senior national title taking out the MX2 class from Australian Jed Beaton (Yamaha). Former champ Kayne Lamont (Yamaha) from Mangakino won the Taupo round on his way to climbing to third position overall.
Ngatea teenager Benjamin Board (KTM) beat Taupo's Wyatt Chase (Yamaha) to the 125cc 2-stroke title.