Their disappointment was in a way justified, with just 13,972 fans turning out - far less than the 23,000-capacity of Brookvale Oval.
The Cowboys seized upon the less abrasive atmosphere of the neutral venue and in the first half their defence was as strong and resilient as it's been all season.
North Queensland ace Johnathan Thurston made his best start to a match since returning from a serious knee injury in round 23, kicking a penalty and laying on the opening try to Willie Tonga with a well-placed grubber.
But it was from a rare Thurston mistake that Manly finally got on the board in the 48th minute and they never looked back.
The Cowboys No.7 tried to give Matt Bowen an inside ball on the Manly 40 metre line, but the ball went astray and Sea Eagles second-rower Shane Rodney streaked away upfield.
Although he ignored an unmarked Jamie Lyon on his inside, Manly made the most of the field position, when a scrum move resulted in winger Hopoate powering over in the right corner.
The Sea Eagles stormed to the front for the first time on the back of a stunning try to fullback Stewart from a Kieran Foran around-the-corner ball just nine minutes later.
Dally M rookie of the year Daly Cherry-Evans was involved in nearly everything as Anthony Watmough, Jamie Buhrer, Hopoate and Matt Ballin crossed in a late flurry which earned Manly a week off.
The Dragons are now safe and, if Melbourne beat Newcastle as expected on Sunday, the Wests Tigers will play the Warriors and Brisbane will host St George Illawarra next weekend.
North Queensland winger Ash Graham was put on report in the seventh minute for a high shot on Manly centre Steve Matai, while interchange forward Cory Paterson was stretched from the field with a suspected cracked vertebrae in the 54th minute.
- AAP
