While there were two atomic bombs dropped on Japan at the end of World War II, I will assume that you are asking about the first one in this question. That is the bomb that was dropped on Hiroshima on August 6, 1945. If so, the answer is that there were three airplanes that were actually over Hiroshima together. Other airplanes were involved in the mission but were not together over Hiroshima with the bomb.
There were four airplanes that participated in the mission but did not accompany or carry the bomb. There were three reconnaissance airplanes sent to determine weather conditions at the various target cities. One was sent to Hiroshima (the primary target) and the other two to alternate targets. Since the one that went to Hiroshima (about half an hour before the bombing) reported good weather, that city was used as the target. One airplane was sent along as a spare in case one of the other airplanes could not complete the mission.
There were three airplanes that actually were over Hiroshima at the time of the attack. There was the airplane carrying the bomb (called “Enola Gay”) and two airplanes with scientific instruments and photographers to record the effects of the bomb.