8 days in Crete

We split our 10 days in Crete, 5 in Chania, 2 in Agios Nikolas, and 3 in Heraklion. We flew into Chania and took a ferry from Heraklion to Santorini. On one of our days in Chania, we took a guided tour, which went up one of the gorges (not Samaria) and down to Elafonissi beach. We thought it very worthwhile, as the driving up that long, steep, narrow, winding gorge road would have meant the driver couldn’t look at anything but the road. The guide was well versed in history and natural history. The beach time was short.
I’ve noticed a lot of sneering when people mention Knossos, but we thought it amazing. There are guided tours that you can join, right at the ticket booth. We had no trouble getting parking in the site’s official lot. There were no other English speakers wanting a guide when we arrived, so we paid the €80 that a group of 8 would have paid. At €40/pp for an hour and a half, we considered it a good value.
One place, off the beaten path, that we enjoyed was the church at Kera Panagia, near Agios Nikolas. It houses a fresco cycle from the 12th - 14th c. We also enjoyed an excursion to Spinalonga, while staying in A.N. There is a sweet folk art museum in A.N. Worth visiting.
If you have more questions, feel free to ask or pm me.

We have similar tastes, although we also do like to be next to the water. Here is our trip report from last June in case you find it useful:
https://community.ricksteves.com/travel-forum/trip-reports/two-week-trip-to-crete-and-greek-mainland

In that report I've tried to mention what worked and didn't work for us. Definitely see the National Museum in Knossos where many of the ancient treasures are now kept. Everything in that museum is of high quality and helps fill in the blanks about the people who lived at Knossos. Both are easily doable in less than a full day. We also saw the Koules fortress (nice) and walked the walls (skippable). After Herakio we heeded south to the Phaestos area to see the palace and nearby Museum of Ethnology. I wasn't sure how I would find Phaestos as I'm not generally as interested in 'ruins' but the setting is so striking it really provides insights into the way the Minoans lived. We wandered the site for hours. There is a little snack bar on site where we got an ice cream and savored the view.

Like almost everyone else, we were completely enchanted by Chania. Great restaurants, full-of-character little bars with live music under the stars, beautiful setting, good shopping, intersting little museums, we also chartered a day sail from the harbor that was a splurge but really fun. I highly recommend the Cretan Renaissance hotel in Chania. Family-run very friendly staff, beautiful rooms.

We also really enjoyed Loutro on the south coast. A lot of Cretans told us Loutro holds special memories of vacations spent with family, and we found it really perfect as well, at least in mid-June. It's a small half-moon of hotels and restaurants with low-rise development. Very laid back and right on the water. It's possible to hop by ferry from Hora Sfakia along the coast going west, or possible to start in Paleohora (I think) going east. I kind of wished we'd also seen Sougia, which can be reached by ferry from Loutro or by a long drive around the national park. If ferry-hopping appeals to you this is an opportunity.

We walked the Imbros Gorge, which is near Hora Sfrakia. I'm glad we did it because it added variety to the activities on our trip but I'll make a heretical statement here and say I could have skipped it, even though I love to hike. With the time we had, I would have instead have stayed overnight at Elafonissi and walked the beach in the evening and morning instead. It is Caribbean-beautiful. Living in the Midwest, getting coastal is always special.

Our advice isn't going to change much from what has already been suggested. However if you can provide us with a bit more information the sequence of the places we are suggesting may change when we understand what your plans are before and after your Crete visit.
Where are you flying from to get to Crete? Where are you going after Crete. Are you going back to Athens, Island hopping or perhaps plan to fly directly to another European country from Crete.

You appear to be interested in Archeological sites so Central Crete might be a focus for you. Heraklion makes an excellent base for some exploration. Knossos and the Archelogical museum are close to Heraklion. The central area of Heraklion is full of old buildings and it has the waterfront Castello and Venetian era harbour.
Heraklion https://www.flickr.com/photos/stanbr54/sets/72157655935354556

A day drive from Heraklion would be south to Phastos and its summer palace at Agia Triada just 4km from Phastos. In my opinion the nearby site at Gortyz/Gortyn (and probably a few other spellings) is a hidden gem just waiting to be discovered. It does have a gated site with a church founded by Titus and a couple other interesting attractions however when you leave that site go back to the parking lot and look down the road. The whole area is olive groves but as you walk along the road you see fallen Roman columns lying on the ground. Eventually you will discover a partially excavated Roman era city. The pratoreum is there with some streets, baths a temple and a buried amphitheater. Its an unbelievable site. You can expect to be there for two to three hours and bring water there are no services.
Knossos, Phastos and Gortyz https://www.flickr.com/photos/stanbr54/sets/72157645085297380/

You might also want to do a long day trip to the east to visit Spinalonga Island. Its a moving site.
Spinalonga https://www.flickr.com/photos/stanbr54/albums/72157661798099198

You mentioned Chania. It has a lovely old town and harbour. Look at the Theotokopolou street area. Its in the old town and has shops, tavernas and hotels in every price range. Its only a two minute walk to all the action of the harbour.
Chania http://www.flickr.com/photos/stanbr54/sets/72157632117917828/
Theotokopoulou St area http://www.flickr.com/photos/stanbr54/sets/72157632118491316/

You might want to visit Rethymnon to see the Fortezza and nearby Meladoni cave with its sad history. Near Chania you can also visit Ancient Aptera, with 5,000 years of history strewn over a mountain top.
Lastly you can take the boat excursion from Kissamos harbour to visit the beaches at Gramovossa and Balos lagoon with a 14th century pirate fortress as a bonus attraction.
Gramovossa, Balos and Elafonissi https://www.flickr.com/photos/stanbr54/albums/72157698932695812

Ancient Aptera, Melidoni Cave and village. https://www.flickr.com/photos/stanbr54/albums/72157672118379637

Thats about two weeks of suggestions so you will have to narrow it down somewhat. The car gives you great flexibility for this trip.

P.S. If you love Greek music or dance and are spending time in Athens, check out the Dora Stratou dance theater in Athens, a self-described "living museum of Greek dance, since 1953."
http://www.grdance.org/en/
The music and costumes are simply amazing and the performances give you a sample of the wide variety of traditions within Greece. The theater is in the central Athena area; it's great after dinner entertainment. We were both captivated. After getting home we bought all their digital music available on ITunes to keep the Greek vacation magic going a while longer. DH and I were just talking the other night about how wonderful that performance was. Just perfect really.