Weather is unpredictable. The days can be windy and sunny, sometimes with overcast cloudy skies. The nights can be chilly and damp. Most shops and restaurants will be closing or will already be closed.

Weather history: http://tinyurl.com/9lgqbnf

Crete will be warmer and sunny... but the water won't be warm for swimming...
Have been 2-3 times in Crete at the end of October, and it has always been very nice.
The weather is very pleasant, some days can even be warm....
Crete has a large permanent population, and all Cretan cities such as Rethymno, Chania and Heraklio are very active and alive

Late October may be a good time to consider the mainland, which never shuts down for the winter, and doesn't have as much wind as the islands. Much as I like the islands myself, I don't like being there when most of the businesses are shut down and it is to cold to eat in outdoor restaurants.

If I had to choose, I would split my time between Athens and the area around Nafplio, which has much to see. If you must go to Santorini, fly there and back for 2-3 nights and spend the rest of the time in Athens.

October is a marvellous month in Greece. Visit the Dodecanese islands, in particular Rhodos and Kos.

The suggestion of Rhodes works. The island is smaller than Crete and much easier to get around.

Islands' charm for most people are the outdoors. That been the beach, or scenery, water sports or walking under hot Greek sun inside thr maze of tiny lanes in each island's Chora, noting the architecture, chatting with fellow visitors, enjoying a meal under a vineyard in a tavern's veranda, in general soak in the summer ambiance. By end of September this ambiance is lost, like it or not. Even on sunny days, feeling is not the same. And there is a large change some days will be cloudy or rainy. What is your plan B then? I am not saying this will not be a nice trip, I am saying that it will be a different trip than saying a July or September trip. Smaller islands with small permanent population will be "shut down" with no visitors around and most Greeks that live on the island on summer will have move to mainland for winter. Very basic infrastructure for year around residents will be available, that might or might suit be enough or a visitor. Locals will have all the time of the world to speak with you, but on my experience October, after a long season, is very different that say April before season. On my experience as an of-season traveler and a person working in hospitality industry my self, people are really tired and warn out and need a break and their own personal time, so less keen to enchant you in long talks.
I am not as familiar with Crete as with other islands mentioned. I agree avoiding beach resorts and focusing on larger places is advisable, I am not sure if this is what you had on mind originally though. Hiraklion for example features some very nice spots and will be lively exactly because it is a major port and all year around destination but it is the 4rth largest city in Greece after Athens, Thessalonika and Patras. Usually people have smaller, more intimate places on mind when talking of Greek islands.

It is important to remember that regarding the weather October is a transition month. This may be a "duh!" statement, but early October is much like September, while late October is more like November. The later in the year, the more changeable the weather will be, and the more likely there will be cloud, rain, and cool temperatures. Personally in October I would rather be on the mainland than on the islands.