The two were not set to give speeches at the site but were due to speak at a televised forum later on Thursday.
Hijackers seized four planes during the attacks, two of which crashed into the towers of the World Trade Centre, while a third crashed into the Pentagon building in Washington DC.
Another hijacked aircraft was brought down in the state of Pennsylvania, killing all on board.
Earlier, McCain had visited Pennsylvania to pay tribute to those passengers who reportedly acted to bring down the craft rather than allow it to reach its target.
They "grasped the gravity of the moment, understood the threat, and decided to fight back at the cost of their lives," McCain said.
Two separate minutes of silence were observed at 8.46am and 9.03am, marking the precise moments when the hijacked airliners struck on September 11, 2001.
Bloomberg said September 11 will "live for ever in our hearts and our history."
The anniversary, he said, is about "New Yorkers, Americans and global citizens remembering the innocent people from 95 nations and territories that lost their lives that day."
The names of those killed in the attacks on the World Trade Centre were read out as part of the commemoration events.
George Bush, the US president, earlier attended a service in Arlington, Virginia to remember those killed in the Pentagon attack.
The Bush administration began its so-called war on terror shortly after the attacks.
|Bush's approval rating has sunk amid the so-called war on terror [AFP]
"One of the worst days in America's history saw some of the bravest acts in America's history," Bush said on Thursday at the Pentagon memorial.
"We'll always honour the heroes of 9/11 and here at this hallowed place we pledge never to forget their sacrifice."
Bush also paid tribute to the US military in for campaigns in Iraq and Afghanistan.
"Since 9/11 our troops have taken the fight to the terrorist abroad so we do not have to face them here at home," he said.
"Thanks to the brave men and women and all those who work to keep us safe there has not been another attack on our soil in 2,557 days," he said.
But the US president has little support from the US public after military invasions in Iraq and Afghanistan foundered.
"I think the president's approval ratings say it all right now; they are the lowest they have ever been for a sitting president," Kristen Saloomey, Al Jazeera's correspondent at Ground Zero in New York, said.
"Also significant is the attempt made by John McCain, the Republican candidate for the presidency, to distance himself from the Bush presidency. His campaign is stressing change and a break from the Bush administration."
The 9/11 attacks remain a deeply emotional issue in the United States, despite polls showing that US citizens are largely concerned about the state of US economy at present.
But the memory of the attacks remain raw, given that no permanent memorial at Ground Zero has yet been erected to commemorate those who were killed in the 9/11 attacks.
Sally Regenhard, whose fireman son was killed while attempting to rescue those trapped in the World Trade Centre, said she wants to see Obama and McCain focus on US security.
"I'd like to hear them say they're going to get more involved regarding... the need to protect our cities from all types of chemical and biological and radiological attacks," she told AFP.
"I want them to get involved with legislation to create a national standard for emergency response after attacks, hurricanes - whatever the emergency."
Michael Chertoff, the US chief for homeland security, said the government had undertaken a raft of initiatives to improve security.
"I don't think there's any doubt that we are safer today than we were seven years ago," he said.
But he warned that al-Qaeda, whom the US has blamed for the attack, remains a potent force.
"Al-Qaeda continues to focus on the aviation system as an area where they want to target," he said, arguing however, that vulnerability has been "substantially reduced."