Unnamed US Officials told the NYT that Kotey, 34, and Elsheikh, 29, were captured by the Kurdish-led Syrian Democratic Forces which were fighting the last remaining pockets of IS fighters near the river Euphrates on the Iraq/Syria border.
It is unclear if the Justice Department will prosecute the two men or when they will be turned over to the USA military, the Times reported.
Mohammed Emwazi, known as "Jihadi John" in ISIS propaganda videos showing beheadings of prisoners, was the group's leader. The fourth member, Aine Davis, is in prison in Turkey on terrorism charges.
Since their capture, both Kotey and Elsheikh have provided important information to military interrogators, the Times reported, citing a "senior United States official". They subjected western hostages they guarded in Syria to constant beatings.
American authorities were informed last month that the militia might have apprehended Kotey and Elsheikh, according to the Times.
The four Londoners were linked to a string of hostage murders in Iraq and Syria during the bloody Islamist uprising.
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"As a guard for the cell, Kotey likely engaged in the group's executions and exceptionally cruel torture methods, including electronic shock and waterboarding", the State Department said in a statement released in January 2017.
Kotey also acted as a recruiter for IS and persuaded several British citizens to join their ranks.
ISIL is another acronym for Islamic State. BuzzFeed News spoke to British and American intelligence officials, obtained identity documents, and interviewed neighbours, relatives, and friends.
U.S. officials were informed in mid-January that the militia might have captured the men, the newspaper reported, adding that the officials later confirmed their identities using fingerprints and other biometric measurements.
Other information has been collected from cellphones and other electronic equipment they were carrying, the U.S. official said. He was killed in a drone strike in Raqqa 2015. Some of their victims included the British aid worker, David Haines and USA journalist, James Foley both beheaded in 2014.
The SDF is an alliance of Kurdish and Arab fighters opposed to IS.