It is time enough to get a taste, some will argue that Crete needs more time, but it is what you have. I would do the trip the following way to maximize time...
Arrive in Athens, depending on arrival time and connections, either spend the night in Athens and get an early start the next day, or go directly to either Crete or Santorini. Plan on flying, do your time there, then ferry to the other island, do your time there, then fly back to Athens for the rest of your trip.
Ferry from Athens to either Santorini or Crete takes most of a day or overnight, eating up time, making flying a better use of time.
For Crete, if possible, arrive in Heraklion, do a night there, visit the Museum and Knossos, then head to Chania for the remainder.
Doing Athens at the end reduces the risk of trying to make connections home.
All this is pretty quick, maybe hectic, but makes a good trip.