The 62-year-old was extradited to the US after he broke out of Mexican prisons twice and was recaptured.
The guilty verdict triggered a mandatory sentence of life without parole.
He added that he had received an unfair trial and accused jurors of misconduct.
Prosecutors said Guzman was responsible for smuggling at least 200 tons of cocaine into the United States and a wave of killings in turf wars with other cartels.
Speaking to AFP prior to the proceedings, Guzman's lawyer William Purpura said: "I think he is in a good state of mind right now".
El Chapo claimed the February trial was unfair, and alleged he was tortured while in confinement.
Complaining bitterly that he was unable to hug his twin daughters, who did not attend the hearing, Guzman said "the United States is no better than any other corrupt country that you do not respect".
Attorney Mariel Colon, who has visited Guzman regularly in prison before, during and after his trial, says she is optimistic about his chances on appeal.
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The drug kingpin was famously caught in January 2016 after an intense manhunt by Mexican authorities and US intelligence officials - the day before Rolling Stone magazine ran a story by actor Sean Penn about the fugitive and his narco empire. Cogan denied that request.
When entering and before leaving the room, he touched his heart and blew a kiss to his wife Emma Coronel, who wore a black and white suit and potentially saw her husband for the last time.
MCALESTER, OK - JUNE 11: Convicted murderer Terry Nichols is escorted out of the Pittsburg County Courthouse after a state jury deadlocked on a life or death sentence for his state convictions June 11, 2004 in McAlester, Oklahoma.
He will be offered the chance to speak publicly before U.S. District Judge Brian Cogan pronounces Guzman's sentence.
In what could be his last time addressing the public before he is shipped to Colorado's Supermax prison, El Chapo told the courtroom "there was no justice here".
There are few men in El Chapo's position that have captivated an audience quite as he has. He has twice escaped from maximum security prisons in Mexico.
Guzman, 62, was convicted in February on multiple conspiracy counts in an epic drug-trafficking case. The Mexican government says he blew his cover through a series of slip-ups, including an attempt to make a movie about his life.
Guzman made a name for himself as a trafficker in the 1980s by digging tunnels under the U.S. -Mexico border that allowed him to smuggle drugs more quickly than any of his rivals.
During the epic three-month trial in NY, jurors heard evidence from 56 government witnesses, with many describing in exacting detail the cartel boss beating, shooting and even burying alive those who got in his way, including informants and rival gang members.