Difficult one. June and September always seem so alike in my mind – much like February and November. The weather's similar, everything's open and really, I'd base my decision on the price of the ticket to get here. Also, remember that as your June stay goes on, the weather's getting progressively better and the people happier, whereas in September, everyone's just come back from holiday, we're broke and a little sadder. the weather starts to get cooler.
As for fiestas, June is probably better in Madrid. We have San Antonio de la Florida – fun but not the best.
OK, I'd say June. It means you have to wait less too.