nice beach end of september

Hello everybody,
I intend to travel from the 25h September to the 30th. The purpose of the journey is swimming in the sea. So I've been wondering where to go.
I’ve read quite a lot about Okinawa Hontô and the islands BUT honestly as I am studying in Tokyo I would prefer a place not so far away.
My question can be summarized to:
What is the cheapest way to stay at a nice place (Guesthouse, Hotel, …) close to a beach that I can still swim in at the end of this September without danger of Jellyfish?

It would be really great I you would share your knowledge with me.

At the end of September, the only places in Japan that I can assure you you can swim are Okinawa and other places that are more inconvenient location-wise.

But if you would like to try dipping into icy cold water, there are several places in the Miura Peninsula that have calm, clean tiny beaches without jellyfish and reasonable ''minshuku'' nearby like Kannonzaki and Aburatsubo. They're just 1.5 hours from central Tokyo by Keikyu trains.

However, if swimming in the sea is your main purpose, it seems like a much better deal to hop on a direct 2 hour flight at Haneda and go to Ishigaki or Miyako Islands in Okinawa Prefecture.