Chani's response was PerfectI (i'm smiling a little because I think she took some of my advice he he). I'm delighted at the timing of your trip -- everything's open, nothing too crowded (except Santorini). I'll just add some commentary to Chani's super-hellpful report:
CRETE - 6 nights (5 days).. u can see a lot. This fab map - http://www.explorecrete.com/crete-maps/images/Crete-eot.png - (click to enlarge) is great for planning. Re Chania, suggest taxi from airport on Arrival Night. Suggest look for room on Theotokoupolou St, a no-cars lane on West side of Harbor; it's PACKEd with many pensions/small hotels; 3 best situated, at seaward end of Theo St, Hotel Hera 4 rooms, Casa di pietra http://www.casadipietra.gr/ 5 rooms, & a bit upscale Hotel Palazzo (ask for front room balconies on all 3). Full Day #1 just exploring Chania (and still not see it all!) Onward options: Day #2AM, Car Rental (they'll deliver to near hotel), drive to top of Imbros Gorge, nice 4 hr trek down (bring folding trek sticks; path is bumpy stony), all floral and fragrant in May (bushes of Thyme!), bring picnic lunc; at bottom walk to taverna, get taxi (usually a pick-up truck) back to car -- on route back u could stop in Rethymnon for a hr just to see Fortezza.
Day #3 - Drive South?? thru Spili... stop @Phaistos? then on to Matala. Beach pensions are meh, I recommend just back from beach Dimitris Villa, lovely landcape, pool, cafe, family-run. Daughter can scale bluff to caves (while you applaud from a beach chair). Day #4-5 ?? - head N E toward Heraklion, possible stop @ Gortys en route - u want to seek Knossos AND Museum & avoid crowds - 1 strategy is to go to Hotel (I like Kronos, right on seafront), drop bags, drive car 1/2 mile to ferry pier (u can see it from hotel, Drop car (no extra fee). Depending on timing Go to Museum (it helps to see the treasures before the ruins), Take local bus to/from Knossos (either 8 am or after 2 pm, to avoid Cruise Crowds). Back in Heraklion, stroll seafront to Huge Fortress, enjoy "meze" dinner feast at waterside taverna (hippocampus?). Day #6 - Ferries leave 9:45 --- Some just to Santorini... others stop @ Santorini, then go on to Naxos.
NOTE -- I highly agree with Chani re Santorini -- the hassle of huge cruise crowds is awful. If you MUST have snap-shots of the "famous Caldera View" ... I suggest a Fast-Fast "glancing blow."... 20 hours! On Noon arrival, check into handy Fira hotel with view.. walk around Fira... cathedral, small but good museum? (Avoid OIA from 10am-4;30pm or so, when it's crammed with Incredible cruise/bus group crowds). Instead, take public bus to OIA to arrive 4:30, leave by 6:30, go to restaurant in FIRA (I recommend top terrace view of "STANI"), for serene sunset dinner. Next AM, check out, get taxi (€15?) to pier for 10:45 Championjet ferry --open back deck to see View on Departure... Another option is 1-day tour from Naxos-Santorine, but the best excursion boat goes only on Wed & that may not work for your calendar.
NAXOS -- What she said. Tell Studios Naxos that Janet sent you, for Unit #1 (which chani had) or if that's booked, #2. There are a dozen ohter places wth balconies right on the sand.. Diogenes Studio, Studios Kalergis, LefKes Studios, Hotel Asteria -- check booking.com. Devote a full day to exploring port town, Kastro, museums, winding lanes. Great bus network - do a full "beach day" @ Plaka - using sunloungers at Aegean Palace. Naxos Sun is good-value allday tour; llunch stop for swims (bring suits!). Also check fab NEW half-day tours - https://philemafoodtours.com
ONWARD -- if you fly in AM to ATH (and have skipped Santorini or given it just 20 hours), you might have 2 nights, 1.5 days to Discover Gorgeous NAFPLIO -- the most beautiful Old Town in Greece. Get car @ airport just 2.5 hrs on Greece's most modern multilane hiway, no stops til after Corinth canal ... I recommend a quick stop (just 5 Km off highway) to NEMEA.