I went there in March 2015, Ishigaki was okay, 24-ish as far as I can recall (outside temperature was between 25 and 27°, I didn't have much problems ad enjoyed my dives without any problem, dives were not too deep either. We spotted BIG mantas at Manta point even though the Instructor later admitted we were lucky as in that month the chance of seeing them isn't particularly high.
Yonaguni was more challenging, weather was so, a bit of wind and no chance to go to the underwater monument so only did hammerheads dives at Irizaki (both time we spotted them but it was mostly diving in the blue, going as deep as permitted and wait to see if they'd show up), water was around 21-22° degrees and back in the boat we'd pour hot water inside the wet suit.
All in all, enjoyable places to dive if in Japan but don't expect wonders when it comes to corals or quantity of marine life.