For the Greek Isles, Windstar is an excellent suggestion. They do sailings from Athens to Istanbul, Rome, Barcelona, or Athens to Athens trips - all of these voyages thread their way through various islands. They have multiple cruises still showing availability in September 2021. SeaDream is another great option - one of my favorites! Likewise, they have two Athens to Athens voyages in September 2021 that have limited availability. Oceania, which we enjoyed immensely, has three cruises departing from Athens in September. This is a larger ship than Windstar or SeaDream - great food!!! Azamara, a relaxed, casual atmosphere, has various cruises in September 2021 that start or finish in Athens. They recently separated from Royal Caribbean (RCCL) and initially had some great deals, although I've not looked lately.
If you want a more intensive Greek Isle experience, stick with the Athens to Athens cruise options, or perhaps work through a charter group. Good luck!