The targets were chosen for their military value.

Internal US discussions at the time show that the US did not believe Japan was heading towards a surrender, and projected immense casualties from either of the other two options (invasion, blockade) to end the war. For that matter, Japan was not 'going toward a surrender' except insofar as their 'surrender' offers included "We keep our brutal colonial empire, otherwise we will fight to the end." Japan was training fucking schoolchildren to become suicide bombers in preparation for a US invasion at that time. That's not 'going toward a surrender'.