Sorry, can't help you on with details of anchorages etc but I'm sure someone will be along soon who can. As an island to visit and explore Crete is a terrific place. The people are extremely friendly (as long as you're not German - they have long memories!) and the scenery is simply stunning. Be sure to try the local raki. It's basically grappa and is powerful stuff....
Good luck with your travels.
I did sail there from Athens a long time ago, we ran down from Thira to Agios Nikolaos which now has a marina and an anchorage at Elounda. Sitea was also welcoming.
I understand Chania is worth a visit, and the southwest coast as long as you're not expecting southerlies!
The problem is the middle, since I understand neither Rethymnon nor Heraklion are particularly yacht friendly.
However it is visited by yachts and some winter at Ag Nik. I hope one of them will contribute since I am planning a cruise there myself next year. Visit JimB's site.
It's a few years since I visited when I spent a couple of months there and left my boat in the marina at Agios Nikolaos - safe and not very expensive.
Rethymnon now has some yacht pontoons and is a pleasant town. Near to Agios Nikolaos there is an excellent anchorage in Spinalonga lagoon which is sheltered on all sides, about 1 mile by 1/4 mile and less than 8 metres deep. Well protected from the sea by prone to fierce gusts of wind. Very safe though.
In settled weather we enjoyed anchoring off Mohklos and in the bay at Sitia. The harbour there gives good shelter when needed.
Crete seems to suffer from very strong winds for much of the summer (I don't know about the winter) so cruising isn't that easy. The island is well worth a tour as it seems to be two extremes - some parts are very touristy but the rural areas are like my memories of mainland Greece from 40 years ago.
I was in Rethymnon a few weeks ago. Not sure on yacht facilities but the old town is a very pleasant place to spend a day or two. Chania is also pretty but not quite on par with Rethymnon.
If you fancy car hire is very cheap and there are some lovely places for day trips.
Raki for sure is worth trying, also Dakos is a Cretian speciality for a side dish or salad. They like their snails too...but I've never been one for those.
If you get to Chania, the maritime museum is worth a visit.
Its a long time since I was on Crete,but if I remember rightly at a place called Georgiopolis, I saw yachts moored along the river as far as the road bridge. At the other side of the road bridge it is called Turtle river, people hire small boats to see the turtles, all the ones I saw were Terrapins. The mooring was free and well sheltered but no leccy or water at the side.
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Harbours. This is a tourist dense island, so prepare for the culture shock, especially in Iraklion. Many charter flights to UK, and internal flights to Athens. A moderate number of UK expats in residence.
Iraklion (3/10) is the gateway to Knossos (9/10), and therefore worth a visit as long as you can stand the crowds and blatant tourism in the town. A new harbour framework has been built at Palaoikastro (north of the town), already well filled with local boats, but with shallow patches less than 2m, so enter with care! Gouves is a full service marina sited below a smart hotel some 6nm E of Iraklion - web site www.portogouves.gr
Rethymnon, (4/10) is also tourist dense, but has a good yacht harbour.
Ayios Nikolaos (5/10) has an interesting setting, restaurant touts and a good marina - a wintering spot for live-aboards. There are many anchorages and quieter places just east, and Spinalonga Island (once a leper colony, worth a visit) is by the entrance to the large lagoon north of Elounda.
West Crete (6/10) At the west end of the island Chania (6/10) has managed to maintain quite a lot of local charm around its harbour and marina, but it is a little cut off by the (busy) firing range activity off Ak Maleka. We enjoyed the (rather windy) west coast anchorages, ending up in the super little harbour at sandy Paliohora (6/10) ( chart ) a quiet little village popular with windsurfers and accessible to the Samaria Gorge - a famous but rather crowded walk down a stunning ravine.
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There's more about Crete winds and weather on the site. People have enjoyed Sitia, out at the eastern corner, and nearby anchorages, but I haven't been there.