You will have to claim and recheck, but...
Last November I transited through Athens on Olympic Air from Skopje with an onward flight to Naxos (all one ticket). They told me I would have to claim my bag, go through customs, and recheck it.
It took a full hour to get through passport control. By the time I got to baggage claim all the luggage from my flight was gone. I went to the lost luggage counter, and they looked it up and told me that someone from the airline had taken my bag, cleared customs, and checked it through to Naxos. Sure enough, when I arrived in Naxos, nervous though I was, it came off the plane.
So that could possibly happen to you, though I don't know if Aegean Air operates the same way.
In any case, assuming your first flight is on time, and assuming it takes you an hour to clear immigration in Athens, and assuming it takes you another half hour to make sure your bag is checked through to Chania, it will be after 8am by the time you are out of the airport. Then you get a driver or taxi to take you to the Acropolis. Say you get there by 9am. (I don't know how bad morning traffic is on a Friday in Athens; maybe it'll be later than that.)
I think you could visit the Acropolis in two hours, so let's say you're done by 11am. An hour back to the airport gets you there at noon for a 1:40 flight. It's domestic, so that might be adequate, but it might by cutting it close.,
It might not take a full hour to get from the Acropolis to the airport, but I'm just rounding up to point out that you can see it may be possible but if I were trying to do it I'd be very anxious.
If visiting the Acropolis is important to you, I'd make it an overnight stay in Athens. That way you can also visit the very excellent Acropolis Museum (https://www.theacropolismuseum.gr/).