We don't know. There is some evidence that he was leaning towards authorizing another strike. But it didn't happen, so we don't really know for sure what he was going to do, or what the target would have been. The most provocative document we have is an account from a British ambassador that says that Truman "sadly" told him that he "he now had no alternative but to order an atomic bomb to be dropped on Tokyo." Later that day, Japan surrendered. It still would have taken about a week to field the bomb once Truman gave the order, though, so it is not quite as tight a thing as it sounds like.

I wrote an article on the question of the "third shot" for National Geographic History last summer, and it discusses this and what evidence we have (and don't have) for it.