Luis Jose-Duarte, 46, was taken into custody for the deadly stabbing of 38-year-old John Sheldon at the Brooklyn Bridge-City Hall/Chambers Street station.
Sheldon was stabbed on a southbound No. 5 train and then exited onto the platform.
Police say it began with a dispute over someone stepping on another passenger's sneakers.
Witnesses say the victim was being aggressive toward the suspect and called him an anti-gay slur.
The suspect allegedly pulled a knife and stabbed Sheldon in the torso.
The suspect left the train at the Brooklyn Bridge City Hall station but Sheldon followed him, at which point he was stabbed again on the platform.
Jose-Duarte is now charged with first-degree manslaughter.
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