"This is the big title I wanted after winning in London, so I am very happy to win here," said Kunieda.
"My forehand was not too good today and Scheffers played a very good match.
"Maybe in the second set I misjudged the medical time-out.
"I was 40-0 up and should have played for one more point, but he won it.
"The final set was just a mental contest and I am mentally strong."
In the women's event Jiske Griffioen of the Netherlands claimed the singles title with a 6-4, 6-4 win over compatriot and world number two Aniek van Koot.
Griffioen, who won the women's singles bronze medal at London 2012 made the most of the absence of 14-time NEC Wheelchair Tennis Masters champion Esther Vergeer as she added her name to the list of five Dutchwomen who have now won the NEC Masters women's title in the event's 19-year history.
"I'm really happy, I had a really good week and beat Aniek in the round-robin as well, but today I had to start all over again and it was a really good match.
"I think it's good that we have a new winner even though Esther [Vergeer] isn't here and I'm so pleased to have this title."
In the quad singles final, American top seed David Wagner overcame Britain's Andy Lapthorne 6-4, 6-2 to take his fifth title at the event.
"It's a real honour to see your name on the trophy more times than anyone else. It's really cool," said Wagner.
"As I've said all week, you've got to be on your game because this is the NEC Masters and you've got the best players in the world here.
"It was a good match, enjoyable to play and I knew he wouldn't just roll over, I knew he fight back with everything he had, so I just tried to stop that and to stay the course."
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