There was at least one aircraft which took an operating nuclear reactor into the air - the NB-36H. It was used as a test bed for the feasability of actually desiging a nuclear fueled engine. It was built from a B-36H that had been damaged by a tornado that struck Carswell AFB in September 1952. The reactor was mounted in the aft (#4) bombbay and the crew was carried in a lead lined capsule in the nose. Canopy was replaced with an airliner style canopy. It made a total of 47 flights (215.75 hrs total), of which 21 (89.0 hrs total) were made with the reactor operating.
On all the flights, the NB-36 was accompanied by a C-97 with a platoon of Marines whose job it was to parachute down and secure the area if the NB-36 crashed (giving a whole new meaning to "glowing in the dark"). Even though the program proved that a nuclear reactor could be operated in flight, cooler heads question if we really needed or wanted to have one in flight and the program was cancelled. Magnesium Overcast by Dennis Jenkins has an extensive chapter (including pics and drawings) on the NB-36H