Samos. You can get off the beaten track on Samos to discover glorious beaches, rugged mountains and traditional villages. It's hot in September, though, with 11 hours of daily sunshine, so avoid too much exertion in the middle of the day.
Crete. Crete is the largest of the Greek islands with areas of superb natural beauty. If you avoid the hottest hours of the day, you should get out to explore the harbour fronts, hiking trails and ancient sites. The sea temperature is perfect for swimming at 23ºC while rain is almost unheard of in September.
At the same latitude as Morocco and Cyprus, the largest of the Greek islands, Crete – famed for its mythical Minotaur and labyrinth – enjoys exceptional sunshine: 300 days a year on average. In October, the mercury is still high enough to tempt swimmers into the sandy inlets along the coast of Ambelos.
Crete is the warmest of the Greek islands in October because of its geographical location in the South Aegean Sea, close to North Africa. While the heat isn't as insufferable as it is during the summer months, it's still a bit intense, mainly if you're not used to mid-20s temperatures.
What are the hottest places in Europe in October? The warmest place in mainland Europe in October is Cyprus (26°C) followed by Malta (25ºC), Dalyan (25ºC) in southern Turkey and the Greek island of Kos (25ºC).
Crete is a much more real and enjoyable place than Rhodes, which is pretty much given up to tourism. I'm afraid that also having visited both islands many times over the past 20 years, I'd have to say that Rhodes can offer just as much history as Crete, given it's smaller size.
1. Crete. Greece's largest and most southerly island, Crete has mild and sunny weather throughout winter; in fact, it has some of the warmest winter weather in Europe with average highs generally around 15-16°C and average lows around 9-11°C.
This one is a close call with both destinations seeing temperatures sitting in the balmy mid- to late-twenties during the summer months. Out of the peak season, the Greek island of Crete warms up as early as May hitting around 25C, while the Algarve isn't far behind at around 22C.
There won't be any cooling rain showers: Crete has zero rain in July and August. This is one time of year when, contrary to what you might expect, Corfu is actually hotter than Crete. Daytime averages in both July and August are 32ºC, so expect some days to be much hotter.
Both countries are very hot during summer, but Greece is some degrees hotter than Spain. The difference between the Spanish and Greek summer weather is that the months of July and August in Greece present some moderate wind.
Both Crete and Rhodes offer a mild climate in winter and blistering heat in summer. There's little difference between the two in temperature, though some argue that Crete is marginally warmer due to its more southerly location. Both destinations are popular in the summer, teeming with sun-seeking holidaymakers.
It is really just a matter of geography and the Meltemi wind blowing down the Central Aegean. Thus the choice is islands out of the Central and Southern Aegean such as Thassos and the Sporades like Skiathos, Skopelos, Alonissos, or the Ionion group i.e. Corfu, Paxos, Lefkada, Ithaki, Kefalonia, Zakinthos.
October is when the tourist season starts to unwind, but many experts regard these last few weeks as the among the very best, and not just because the weather is starting to get miserable at home. In the Greek islands, the sun will almost certainly be shining all day and the sea will be deliciously warm for swimming.