I’d suggest that if a school super-scores, you submit all of them. These schools generally claim that they really do just use the super-scores, and often that they are recorded by the school on the report with the super-score numbers, so readers don’t even see full scores. Your scores are fairly consistent anyway, so there’s no real downside. And most schools place little or no weight on the writing scores.
The math is really simple on the ACT. You add up your best components and divide by four. The scores are rounded up if a student’s score ends in .5 (at least by the ACT people). By my math, your super-score, using all three tests, would be a 31.5, which rounds to a 32. Using the last two (June and September), only yields a 31.25, so a 31.
If a school does not super-score, I’d send the June and September results. April doesn’t really hurt you, but doesn’t help either. And you’d have to pay to have the April scores sent to non-super-score schools.
Most schools do not superscore ACT for an obvious reason. It adds cost to students. Your second score is slightly better. Not only the composite is 1 point higher, the lower score in science section matters less in general. However, for schools that require writing in the same sitting, you have no choice. Make sure you include writing in your future retake unless you are absolutely sure you would not apply to any school requires it.