We will be touring Greece the first two weeks in October. Is it too late in the season to visit the island of Naxos or Santorini?
No, not late at all. In fact, Santorini was still crowded when we visited in October.
The weather in Greece is generally quite mild
I lived in Athens for about a year some 30 years ago,.
In January of that year it snowed and the people went crazy with joy--heaped piles of snow on the tops of their cars, helped their children to make tiny snowballs.
Of course because snow is so rare in southern Greece, everything just collapsed--no reliable public transportation and so on, but it was an interesting experience.
Enjoy your visit to the islands.
We were in Naxos first week of October last year. It was sunny and warm. It got cool at night so a light sweater or jacket may be necessary. The temperature was just about right for hiking and touring mountain villages.
One thing though the resort area at Plaka beach was basically shut down by the end of the week. We ate at three tavernas on their last night and we were the last guests at our hotel they closed the doors as we left. All that to say you will want to get a hotel at St George beach. It is part of Naxos town so you can spend as much time on the beach as you want then in 10 minutes can be in Naxos town which will still be lively until the end of the month.