The motorcyclist rear-ended a minivan as they approached Exit 60, Suffolk police said.
The motorcyclist, a 52-year-old man, was in critical condition with head injuries and airlifted to Stony Brook University Hospital, police said. The minivan driver was not injured.
No charges were filed, but the investigation was continuing, police said.
The crash happened about 4:55 p.m., and the rush hour traffic was stop and go, police said.
The LIE closure started at Exit 57, near the Motor Parkway in Hauppauge, and stretched to Exit 60 by Hawkins Avenue in Ronkonkoma, sheriffs said.
State traffic maps showed the backup went all the way to Exit 53 and the Sagtikos State Parkway in Edgewood.
The state Department of Transportation said the lanes were reopened by 7:11 p.m.