The plan was for the shuttle, coming from Washington D.C., to fly over Manhattan several times before landing at John F. Kennedy International Airport.
But because of the size, the shuttle is sensitive to precipitation, and NASA officials decided to call of Monday's flight.
Officials said they will review weather forecasts and announce a new flight date "as soon as practical."
In the weeks after landing in New York City, the shuttle will be placed on a barge and moved up the Hudson River to the Intrepid museum, where it will become part of a permanent exhibition scheduled to open this summer.
On Tuesday, the space shuttle Discovery, also sitting atop a 747, made several flyovers around Washington, D.C. Discovery will be displayed at the National Air and Space Museum of the Smithsonian Institution.