Arrive at Athens Airport the last Sunday of the month, 9:15am. Buses from the airport to Nafplio.
Sunday, Monday, and Tuesday nights in Nafplio. Bus day trip to Mycenae on Monday or Tuesday.
Wednesday night: sleep on the ferry (Bus to Pireus. Ferry to Heraklion. Ferry leaves at 9:00pm. Intending to arrive at Pireus by 7 or 7:30pm).
Thursday: arrive in Heraklion. Archaeology museum. If time, bus trip to Knossos on one of these days.
Saturday night: ferry back to Pireus.
Sunday: Commuter or subway train, and local bus, to Σταθμοσ Αττικησ, Bus to Delphi; first and second buses leave at 7:30am and 10:30am. View Delphi museum and/or the outdoor site. Sunday night in the town of Delphi
Monday: See the rest of Delphi. Long distance bus, and local transportation, to hostel in Athens. Last 2 buses leave Delphi at 4pm and 6:45pm
Monday, Tuesday, Wed, Thurs, and Fri nights: sleep in Athens
Alternative itinerary starting from the first Thursday:
Arrive in Heraklion Thursday morning. Bus trip to Knossos. Archaeological museum if time. Thursday night: sleep in Heraklion.
Friday: Archaeology museum if not seen yet, and/or the rest of the Archaeology museum, and/or Castello del Molo (Koules)
Friday night: Ferry back to Pireus.
Saturday: Commuter or subway train, and local bus, to Σταθμοσ Αττικησ, Bus to Delphi; first and second buses leave at 7:30am and 10:30am. View Delphi museum and/or the outdoor site. Saturday night: sleep in the town of Delphi
Sunday: See the rest of Delphi. Long distance bus, and local transportation, to hostel in Athens. Last 2 buses leave Delphi at 4pm and 6:45pm
Sunday, Monday, Tuesday, Wed, Thurs, and Fri nights: sleep in Athens. If I run out of things to do, Bus day trip to cape Sounion.
Are you sure there is enough time to see both the Archaeology museum, find a grocery store, and see the archaeology museum, in one day?
I probably will go against recommendations and skip Chania.
If I had almost 3 days in Heraklion, suppose I took a part day trip to the palace of Malia near the north coast, east of Heraklion? Or I could have 5 whole days in Athens and see one or more additional less popular museums, and so on.