The final say over extradition and which U.S. court would try Guzman first is up to Attorney General Eric Holder, who has not made a decision.
One federal official told ABC News that there's "an expectation" that if Guzman is extradited, he would be sent to New York to face trial in Brooklyn federal court.
"We are fully expecting to prosecute him in Brooklyn," one official told ABC News.
As in the case of high-value detainees in terror cases, New York is often viewed as the prime venue because the Justice Department has the infrastructure, security and media accommodations there to handle trials of international significance with dangerous defendants.
Other U.S. attorneys, including those in Chicago, San Antonio and Washington, D.C., would also like the chance to try Guzman.
Guzman, whose nickname is slang for "shorty," is the alleged CEO of the Sinaloa cartel, which is estimated to move 25 percent of all illegal drugs entering the U.S. through Mexico. He is facing drug trafficking and multiple other charges and is wanted in at least six U.S. districts and Mexico.
The cartel is also heavily involved in crime and carnage arising from the bloody drug war that has swept Mexico and the U.S. over several years.
Last February, the Chicago Crime Commission branded Guzman the first "Public Enemy No. 1" since Al Capone, leading to him being dubbed as "El Chapone," in the shadow of Chicago's other great criminal.
The DEA has said in the past that as much as 90 percent of the marijuana, cocaine, heroin and other illegal drugs sold on the streets of Chicago are supplied by the Sinaloa cartel. Guzman is also charged with drug trafficking, murder, kidnapping and other crimes in New York.
The alleged drug kingpin has also long been ranked among the richest men in the world by Forbes and drug enforcement experts had conservatively estimated the cartel's revenues at over $3 billion annually.
Before his infamous 2001 Mexican prison escape, Guzman had been serving a 20-year sentence for bribery and criminal association.
ABC News' Pierre Thomas and Josh Margolin contributed to this report.