It depends by what you mean by "unusually quiet" - most people who go there actually hope for fewer tourists as these islands are best enjoyed without the crowds (in July and August when almost the whole of France goes on holiday).
As for the water temperatures - October isn't really the month for swimming in the Med, at least not for too long (though some poeple do enjoy frolicking in the waves if the sun is out). If you have a wetsuit there should be no problem but it could be a bit chilly just with a bathing costume I would have thought, at least if you are thinking of spending some time in the water and not just a quick dip.
Personally I visited both islands out of season (february) and found them to be delightful. I didn't swim though.
Also most people who go there are on day trips, there will be fewer tourists if you spend the night.