As you say, there were exceedingly few Japanese taken as prisoners of war by the United States. Some sources say that as few as 5,000 were taken by the US and brought to actual camps in the United States.
Of course, some Japanese were not allowed to surrender by US troops. It is not surprising that soldiers in the heat of battle would kill some enemy who were attempting to surrender. So I will not claim that all Japanese attempting to surrender were treated well at all times. However, the general situation is that Japanese POWs were treated well.
One reason for this is that good treatment of the POWs is said to have yielded a good deal of intelligence. Japanese soldiers were trained to expect terrible treatment at the hands of the enemy and tended to react well to kind treatment. In addition, they were not well trained in trying to resist interrogation because they were not supposed to be captured. The Americans treated them well and got intelligence in return.
For those few who made it to prison camps on the US mainland, treatment was good. The Japanese, unlike European POWs, were not made/allowed to work outside the camps for fear that they would be targeted by angry Americans for violence. However, the conditions that they experienced inside the camps were, like those experienced by German and Italian POWs in the US, quite good.
For more on this subject, see if you can find this book.