Nicks caught touchdown passes of 80 and 11 yards, as the Patriots (16-0) extended the nation's longest winning streak to 92 games.
It was the third time in four years the Bears (13-3) fell to Independence in the title game.
Prior to both scoring receptions, Nicks suggested the play calls to his veteran coach, who coached the Patriots to four of their five straight titles.
Patriots quarterback Darryl McFadden threw for nearly 275 yards and two touchdowns – both to Nicks, who finished with eight receptions for 205 yards.
Nicks was also a force at safety, causing several violent collisions with New Bern ball carriers.
Independence jumped out to a 17-0 lead on a 34-yard field goal by Brad Barnhouse, followed by touchdown runs by Jeriando Kasey and Cameron Henegan of nine and three yards, respectively.
But New Bern answered on a 27-yard touchdown pass from quarterback David Towernicky to Darryl Reynolds, and trailed just 17-7 at the half.
After the Bears missed a field goal attempt early in the third quarter, McFadden found Nicks on the Patriots very next play for their 80-yard touchdown hookup.
"We were going to run that play earlier in the game; we call it the ‘Flood,'" Nicks said. "I told Coach, ‘The Flood is going to work.' He was kind of thinking twice about it, but before we could run it, we got a penalty.
"So we had a chance again to run it, and I said, ‘Coach, the safety is going to bite down.' That's just what happened, and I ran a post and we scored. I was determined not to fail."
"I told him that was a ‘Big Man run,'" Knotts said.
New Bern cut the deficit to 24-13 following a one-yard touchdown run by Towernicky, but that is as close as the Bears would get.
Two Bears' turnovers in the fourth quarter led to two quick scores by Independence, which won going away.
"This feels so good, especially with the coaching staff we had and all the things we went through together," Nicks said. "This is something I'll always remember."
UNC wide receivers coach Dave Brock attended the game.
Nicks, 6-foot-1, 210 pounds, committed to the Tar Heels on August 2. He said his verbal promise to Carolina is and will remain firm right up until Signing Day in February.
And now with his high school football career behind him, he is ready to focus on the next level.
"I'm going to rest until about January, and then start speed training and lifting weights," he said.
Nicks said he has decided not to play basketball this season.