I believe that it is still Nagasaki. The second bomb was supposed to have been dropped on a city other than Nagasaki (I can’t think of the name), but because of the cloud cover that day the alternate target was selected — Nagasaki.
The arsenal at Kokura was the other potential target, but I believe it was saved by cloud cover.
On May 10–11, 1945, the Target Committee at Los Alamos, led by J. Robert Oppenheimer, recommended Kyoto, Hiroshima, Yokohama, and the arsenal at Kokura as possible targets.