Bloomberg on Tuesday said he spoke to Obama and his chief of staff, Jack Lew, and told them the city would "love to have him, but we've got lots of things to do."
Bloomberg said that he wasn't trying to "dis" the president and that his trip to New Jersey on Wednesday would represent the whole region.
He also spoke highly of the relationship between federal and local officials. He said that on a conference call with the president and other mayors and governors of affected areas, everybody kept saying, "Thank you for the service."
"You know, there was a lot of criticism with (the Federal Emergency Management Agency) back in the (Hurricane) Katrina days, and today, you hear nothing but good things about FEMA, and they certainly have been very helpful to us," Bloomberg said.
The White House said the president and Lew spoke to Bloomberg to let him know the president planned to travel to New Jersey and to ask the mayor if he agreed with their assessment that Wednesday would not be the right time to visit the city.
The White House typically coordinates with local officials before traveling to a disaster zone to ensure it's not drawing away any law enforcement and emergency management assets being used in the disaster response.
Tuesday's storm killed 18 people in New York City, the mayor said. It knocked out power for hundreds of thousands more, plunging the city into darkness.