In Japanese, "kun" is more casual and usually used for friends or those on the same level or lower in the "hierarchy" while "san" is more formal and used for those higher up in the "hierarchy" (older, in a higher grade at school, or in a higher-up position in the workplace.)
It seems that Naegi is a lot closer to Aoi than Togami. He spends a lot more time with her in Danganronpa the Animation and is together with her the whole time in Danganronpa 3: Side Future. They are also in the same grade.
It seems to me he should be calling Aoi "chan" and Togami "san" if anything.