Aside from the "they didn't have nukes in time" answer (covered in the FAQ answers), I just want to address the oddness of the question. The bomb was never developed as a "punishment." While latent resentment for Pearl Harbor played a role in the end of the war discussions, the bomb wasn't dropped on the Japanese because of outright animosity, per se. It was dropped because it was thought it would have a profound psychological effect on the Japanese, and the rest of the world. One can agree or disagree with that as a good motivation for mass slaughter of civilians, but it wasn't about "punishing" them for horrible activity.

By the time the Americans had any nukes ready, the Germans were already mostly out of it. u/restricteddata explains more in this thread, along with some speculative scenarios, and also in this thread, in conjunction with u/QuickSpore.