He arrived in New York on a flight from Cuidad Juarez.
Mr Guzman, who could face life in a US prison, is wanted on charges of drug trafficking and smuggling vast amounts of drugs into the country.
The leader of the Sinaloa cartel was facing two extradition requests - one from California and another from Texas.
Last year he was moved to a prison in Ciudad Juarez, which lies just across the border from El Paso in Texas, but authorities at the time denied the transfer was a precursor to extradition.