It went off without a hitch as 47,000 runners raced through five boroughs and passed cheering crowds. Last year's marathon was canceled because of damage from Superstorm Sandy.
Police were especially focused on security in part because of April's bombings at the Boston Marathon, which left three people dead and more than 260 injured.
At least 1,500 cameras were positioned along the route to help boost security, New York Police Commissioner Ray Kelly said.
There were baggage screenings and surveillance helicopters. Runners were screened and inspected before taking their starting positions, according to police..
Bomb-sniffing dogs and scuba divers scanned bridges and shorelines. Counterterrorism officers escorted ferries carrying runners.
Priscah Jeptoo of Kenya won the marathon's women's division with an official time of 2:25:07. On the men's side, Geoffrey Mutai of Kenya won with an official time of 2:08:24.
Each will get $100,000 in prize money.
In New York, spectators watching from grandstands and family reunion areas were subject to baggage inspections and screenings as a precaution.
"The safety of runners and spectators has always been our highest priority," New York Road Runners, the organizers of the event, said in a statement.
Runners took it in stride.
"It will obviously cause some problems for us, but that doesn't matter," said Runar Gundersen, who was to run his 35th New York Marathon this year. "Security must come first, so I gladly accept delays. ... I think most runners do."
Organizers said a lot of additional security measures will be taking place in the background.
"I know that it's impossible to protect 26.2 miles of road 100%," Gundersen said. "The feeling about that is much like it was in 2001 after 9/11."
CNN's Allison Malloy and Susanna Capelouto contributed to this report.