The No 10 made no mistake from out in front and Waikato extended their advantage to 10 points after 15 minutes.
Next, Cruden pounced on an Auckland mistake and found prop George Dyer in support.
When going to ground, Dyer had the ball ripped from his grasp.
The ball fell for Sinkinson to toe on and he chased down the ball to score his second try, stopping the ball before it went dead.
Cruden added the extras and Waikato had a 17-0 lead at the midway point of the first half.
However, Auckland struck back right away for their first points of the game when flanker Anton Segner crossed next to the posts.
Zarn Sullivan was successful with the conversion and reduced Waikato’s lead to 10 points.
Following that, Auckland were penalised at scrum time in their own half, giving Cruden another opportunity to add three more points to Waikato’s score.
He was successful and Waikato pushed their advantage back out to 13 points with 10 minutes remaining in the first half.
Cruden then added a try to his scoring tally when he pounced on another Auckland mistake, toeing the ball through and then running on to regather the ball and slide across for the home team’s third try.
He added the extras to his try and Waikato extended their lead to 20 points with three minutes remaining.
Waikato were not done yet with first-half scoring.
Flying winger Aki Tuivailala was found in space and he raced away down the sideline to score as the halftime hooter sounded.
Cruden missed the conversion but Waikato went into the break with a 32-7 lead.
In the second half, Auckland looked to mount a comeback, scoring two tries, with Nigel Ah Wong and Millennium Sanerivi both finding their way across the try line.
Sullivan added the extras to both tries and Waikato’s advantage was reduced to 11 points with 20 minutes to play.
The points for Waikato dried up in the second half, but Sinkinson did manage to complete his hat-trick when he picked off an Auckland pass 50m out and raced away to score under the posts.
Reserve Tepaea Cook-Savage added the extras, cementing Waikato’s victory 39-21.
Waikato 39 (Daniel Sinkinson 3, Aaron Cruden, Aki Tuivailala tries; Aaron Cruden 3 conversions, 2 penalties, Tepaea Cook-Savage 1 conversion)
Auckland 21 (Anton Segner, Nigel Ah Wong, Millennium Sanerivi tries; Zarn Sullivan 3 conversions)
HT: 32-7.