Three or four years since we left that area, but just to get things started:
I know of lots of yachts that've been left afloat over winter without any hassle from the Authotities, indeed I don't know of any that have had a problem.
The best marina options would be Corfu, Levkas, or down the Patras Gulf at Missalonghi; if leaving the boat
for several months, my own preference would probably be Levkas. Though Messalonghi would no doubt be a slightly cheaper alternative, unless the Marineiros there have learned a lot, you couldn't rely on them to do much in the way of checking/adjusting lines if necessary; then again, there always seemed to be an overwinter livaboard community in Messi, so if you ask around, someone'll no doubt keep an eye on the boat for you - I watched/checked two the winter we spent there.
If you decide to lay-up ashore, then there are lots of choices: Messalonghi, Nidri, Vlikho, Levkas, Preveza being the larger ones; prices were all much the same when we were there and my preference would be overwhelmingly for one of the Preveza yards (we used Yanni's Aktio yard) being across the estuary from the town proper, they're not as handy/accessible if you're on board, but as a lay-up and leave yard, they're perhaps the best we've used in twelve years cruising.