Nageeye, a 35-year-old Somalia-born Dutchman who was second in the Tokyo Olympics marathon and third in New York in 2022, won in an official time of 2hr 07min 39sec.
"I knew this was my day," Nageeye said.
"I was so focused. Everyone tried to move and I was behind them. You're not going anywhere. This is my race today."
Nageeye defeated Kenya's Evans Chebet, the 2022 New York champion, by six seconds with Kenyan Albert Korir, the 2021 New York winner, in third on 2:08:00.
In the women's race, Chepkirui won in 2:24:35, pulling away late to defeat defending champion Hellen Obiri by 14 seconds with Vivian Cheruiyot completing a Kenyan women's podium sweep in 2:25:21.
"This means a lot to me," Chepkirui said. "It means my training has been good and I'm so happy.
"I had to dig deep. Towards the last, one mile, it was really hard, but I pushed myself to the limit."
More than 50,000 runners competed over the 26.2-mile journey across the city from Staten Island to the finish line in Central Park.
Nageeye did not finish at the Paris Olympics but poured that disappointment into training that produced his triumphant New York effort.
"Every day I was thinking about the Olympics, but I have to do my training. I have to come back. I have to go to New York, at least podium, but my goal was to win," he said. "It looked simple but hard work was behind it."
During the race, Nageeye said, he could not believe how well he felt as the miles elapsed.
"I checked my watch, I was seeing the miles coming, I use kilometers, and I was unbelieving," Nageeye said.
"When I saw 39, 40k and I was feeling like this, I can go onto 50k. I was so focused that when I going to the finish I was like, 'I'm going to win. I'm going to win.'
"The emotions were not there at that moment, I was just thinking I'm dreaming."
Tola fourth
Reigning Olympic champion Tamirat Tola of Ethiopia missed his chance at becoming the first man to win at New York and take Olympic gold in the same year as he finished fourth, 32 seconds off the pace.
Kenyan Geoffrey Kamworor, the 2017 and 2019 New York champion, was fifth in 2:08:50.
Chebet, a two-time Boston Marathon winner, surged at mile 16 and by mile 20 the pack was down to the final five.
Tola dropped back in the 22nd mile and Chebet and Nageeye were side by side down the stretch until the Dutchman surged ahead at the 26-mile mark.
The women's race became a fight between Obiri and Chepkirui over the final mile, Chepkirui pulling away in the home stretch.
Obiri, who took bronze at the Paris Olympics, missed the chance to become the first back-to-back New York women's winner since Kenya's Mary Keitany won three in a row from 2014-2016.
