Flight 4539 from Toronto first tried to land about 8:20 a.m.
"Our airfield crews witnessed sparks during the landing, and then the aircraft pulled up," Logan spokesman Richard Walsh said. Debris also may have fallen from the plane during the attempt, he said.
Mechanics on the ground checked the landing gear twice when the plane flew by the airport, and no problems were found.
The plane carrying 37 passengers and three crew members landed without incident about one hour after its first attempt.
A message left for American Eagle was not immediately returned.