If you decided to stay 3 months in Greece, just in one city, which city will you choose?
My husband and I are planning to stay in Greece September to November, just to be there as much as possible as a local. We are a quiet couple who love to experience new cultures..We would rent an airbnb apartment.

I think you need to give a lot more information to get meaningful answers. What are your interests? What do you want to see? Do you want a place with good connections for public transportation or will you have a car? Etc.

When you say “city” I assume you mean a large urban area. There aren’t many cities on the islands, and to get from one island region to another often means going through Athens.

I would choose Santorini as it has so much to offer. My friend lived there for a year, and I have heard a lot about breathtaking sunsets, unique architecture, and awesome local food. So it sounds like a perfect spot to stay for a couple of months.

I would be torn between choosing between Chania, Crete or Napflion on the Peloponnesian Peninsula.
Two nights on Santorini would be enough for me.

Nafplio
Thessaloniki

Your choice depends upon whether you just want to spend the three months staying in that one place, or if you want to do some travelling as well. Most islands are poorly connected with anywhere else except others nearby and to Athens. If you have any health issues, many islands have limited medical facilities.

Nafplio would be a good choice if you don’t want to stay in Athens. Note: the f comes before the p in Nafplio.

Ioannina
Chania
Nafplio
Corfu Town
Kalamata
Volos, the gateway to Pelion

Chania is widely considered by Greeks & foreigners to be the most beautiful Old Town in Crete & 2nd in Greece -- the country's most beautiful Old Town is Nafplio, hands down. Both have large permanent populations there and in the adjoining newer aress of the towns ... there are academic institutions, museums, cultural events that make the fall vibrant and interesting for a longer stay. Nafplio is accessible from Athens via the most modern highway in Greece... also an excellent intercity bus. Within Nafplio, local bus network is useful, so no need for long-term car rental. Ditto for Chania ... easy bus trip to Rethymnon to the east, which has Crete's major university... again, giving activity and liveliness year-round. Cosmopolitan atmosphere in both places, many ex-pats, also welcoming to short-stay folks like yourself.