How many weeks do you have... and are you willing to rent a car for part of the time? It will be very helpful in Crete ... and also in exploring the Argolid in the Peloponnese, which is so Packed with fabulous archeological sites. You have selected the very best time of year to do this .... I've done 12 extended trips to greece, 11 of them in late may - Late June. Perfect weather, everything's open, nothing is crowded.
The first advice is to purchase & immerse yourself in ROUGH GUIDE to GREECE and BLUE GUIDE to CRETE. The R STEVES guide to ATHENS & PELOPONNESE is good straightforward mainstream D-I-Y advice; (and he has good free audio downloads); however the others give in-depth background &context not in Steves materials, which will enrich the experience immeasurably for travelers like you. You have the time, enjoy the planning. Many other resources to suggest
The most time-efficient way to see the most, without rushing or backtracking, would be roughly as follows:
• Arrival: fly in & immediately take domestic Flight to CHANIA, Crete
• CRETE - 1 week at least: CHANIA & surroundings (Byz & Minoan) - drive to PHAISTOS area, then to Heraklion/Knossos. BLUE Guide will help you choose priorities. Leave Knossos till end. Daily 9:45 ferry to Santorini.
• SANTORINI - 2-3 days, depending. Akrotiri is fascinating, needs prep to appreciate. Ferry to NAXOS
• NAXOS - 5 days? Ruins galore + Byzantine. BEST Museum in Cyclades; priceless Minoan-era statuettes. Day Excursion to DElos... OR ferry to Mykonos, do Visit to Delos from there. Ferry Mykonos to Rafina.... bus to Airport for rental car
• MAINLAND - PELOPS - 7-10 Days Counterclockwise Loop for Monasteries, Mycenae, Classical. Nafplio - Mycenae - Tiryns - Asine - Epidaurus. Mystras, Messine, Pylos, up West coast to Olympia, Rio Bridge to Mainland & Delphi etc.
• ATHENS as GRAND FINALE - 4 days minimum.
NOTE: Santorini doesn't need car, Naxos good bus network, rent car perhaps 1 days for efficiency, otherwise busses. I've done the Peloponnese several times via bus, but only a few sites per time ... if this is your One Shot, car is best plan.