Emergency workers took the Piper PA-28 off the northbound lanes of the Major Deegan Expressway in the Bronx on a flatbed truck at about 6 p.m. Saturday.
The city's Office of Emergency Management says drivers should expect residual delays.
The plane was headed back to a Connecticut airport after touring the Statue of Liberty when it experienced engine trouble and set down on the highway at about 3:20 p.m, New York Mayor Bill de Blasio said.
The pilot and two passengers aboard were being treated for non-life-threatening injuries at a Bronx hospital, de Blasio said.
He called the safe landing extraordinary and "a bit of a miracle," that nobody was seriously hurt or killed.
Patricia Sapol, 29, of West Point, N.Y., was driving south on the highway with her husband when they saw emergency vehicles surrounding the downed plane, about 15 minutes after the landing.
"We couldn't believe it! We thought, 'Oh my god that's a plane!' It was pretty incredible," she said. "The fact that there was no actual crash we thought was pretty surprising."