It really depends on the actual campsites that are available. In general, the campsites in North Pines are smaller than the ones in Upper Pines, but there some really nice campsites in North Pines that border the Merced River.
It also depends what your hiking plans are. Upper Pines is closer to the Happy Isles trailhead but North Pines is closer to the rest of Yosemite Valley. The campsites in North Pines also tend to be a bit warmer during the day because they get more sunlight than most campsites that are located in Upper Pines.