(1) If you are connecting to an international flight on the same ticket, you don't need to go through immigration for a 5-hour transit in NRT.
(2) Even if you do, there is really no reason for them to care about your transit in the US, but the worst case scenario is that they might ask to see the other passport in which case you just show them. (This happened to me once in Korea when I boarded the plane on one passport and entered Korea on another; I guess the officer was confused that my passport didn't match whatever his records showed. But in Japan, I have boarded with one and entered with another and nobody batted an eyelash...)