It was too slow for truly safe deployment and couldn't accommodate the MK3 bomb IIRR.I would use the Lancaster bomber. It actually was better suited to dropping an atomic bomb than the B-29 was. With that, the Allies could have hit anyplace.
If I were in charge, I would start with Berlin. Yes, it kills the leadership. It would kill all command and control. Individual generals in the field would be lost without orders. Would Germany have been able to coordinate a war without Berlin? Would the soldiers in the field fight on when they find out that the capitol of the Reich was gone? Many wouldn't. Hamburg was another logical alternative. That would kill imports. Of course, that had been pounded over and over. Or you could pick a city on the Ziegfried Line and blow it and the nearby section of the line up. Cologne or Dusseldorf maybe? Both are in pretty level areas so that would aid the blast.
Stuttgart is bordering mountainous, lots of variation in height. Not as good for the shockwave spreading. I don't think Munich would be ideal either. It's up high enough that the AA guns are more likely to get lucky at like 600 meters. It's 500 meters closer to the target than Cologne. Terrain wise, Berlin would be best at 40 meters and pretty darn flat. Of course, it would be the best protected place AA wise.
Destroying Berlin is a bad idea, for the reasons given previously.