There is not really any "bus station" in Fira ... just a bus lot, and a little kiosk.
As I remember from an earlier query, I believe that the Pelican Hotel, right on the small town square there, offers luggage storae for a fee. I suggest you e-mail them and inquire. If you do not hear from them, I suggest you just take the bus (with all the others) from the port to Fira town square, and go into one of the area hotels that has an manned reception desk and ask if you could leave your bags for however many hours, for a fee. Don't expect to see a lock-up facility;if they have an area for bags that should be good enough; after all, u will be carrying anything valuable in your day pack.
or..many travel agencies will hold your luggage for a fee as well. Just make sure of their hours, so you get there well before they close! Have fun!
There are some travel agencies in the port that could keep your bags but most of them are open for not too many hours during the day. Maybe try to leave your baggages in the office of Hellenic seaways at the port if it is open the times you want to travel. Actually it is the only office that is open many hours in Athinios port.
Otherwise take the baggages in Fira with you. There as mentioned you will find many place to leave them.
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