Making the most of our time in Crete?

You are going to have to make hard choices. We were in Crete for 11 nights and had to do the same.

But here are a few ideas.

We stayed in Archanes not Heraklion. It is a much smaller rather charming town. We liked it there a lot. You could rent a car at the airport and drive to Archanes for two nights. Go to Knossos the next morning. Then go to the museum. We had been driving a lot by then and were pretty tired of it so we left our car in parking lot and took bus to museum. It let us out right by the museum. We had brought a lunch and ate it in the museum garden. We explored the city afterwards and then took bus back to get out car. We drove back to Archanes for dinner.

Another small (really small) town we stayed in was Thornos. We stayed at Aravanes for one night which we immediately regretted. It is so lovely. You could stay there two and explore parts of Amari valley or go into Rethythmo. We were there in 2022 after the pandemic and drove through the Amari valley to Zaros. We had a great lunch in Amari at the only one restaurant we found. Hopefully it all has recovered some now but the whole area looked pretty depressed. Amari had a few nice sights but I recall going to other towns that had almost nothing open.

You could then go to Chania which is quite lovely. Stay in the old town. We didn’t have a car there but one could be useful if you want to make day trips. We went (after we left) to a lovely olive oil factory and a winery that are day trip driving distance from Chania.

Another possibility is to skip Amari valley and go down to southwest coast. There you have to park your car and take a ferry. You could go to Loutro and spend a couple of nights. We didn’t go there but my son did and he really liked it. We went to Sougia which is wonderful too. You can drive there unlike Loutro.

We liked Thornos a lot but were enchanted by southwest coast. But it is further and as I count you only have six nights.

You are correct Seajet Power Jet is the only ferry on that route on the 16th. Its a large fast ferry. While the passenger area is fully enclosed I believe there is a place at the rear of the ship where you can go outside. Its really windy there but you might want to find a spot as you enter the Caldera at Santorini. Its pretty spectacular.

I suspect the archaeological museum will be closed when you arrive. Seeing the museum before visiting the site is a good idea. Generally best time to visit Knossos is at opening and an hour before closing. Two reasons its hot and the tour groups arrive mid morning and depart later afternoon. Given you are visiting early season that many not be a problem . Knossos has been partially restored. Personally I liked to see what it might have looked like some people are not happy at all with the restoration. Phaestus on the other had has been excavated but not restored so you will see the ruins as they were found.
While you are in that area you might want to look for the nearby Roman ruin at Gortyz or Gorten. There is a gated sight there wort visiting but the real thrill happens when you walk along the road through olive groves. There is a whole roman city partially excavated in the olive groves. You can find baths, streets, temple, walls, some buildings and the governors pratoreum along with a statue. As it is still an active archaeological site it is not open to the public but you can certainly see everything from the perimeter.

Matala on the coast is a good spot to stop. It still retains its hippy vibe.

Sorry I do not remember much of the drive through the Amari Valley we did it in a day driving straight through on our way to Plakias. One highlight that was extremely moving was the visit to Meladoni cave near Rethymnon.

If you have time you might like to stay a night or 2 in Chania. Staying within the walls of the city in the old town is a delight.

These are a couple of album from that trip.
Gortyz https://www.flickr.com/photos/stanbr54/albums/72157666456665788
Matala https://www.flickr.com/photos/stanbr54/albums/72157687857502721
Ancient Aptera near Chania and Meladoni Cave in Rethymnon area.

https://www.flickr.com/photos/stanbr54/albums/72157672118379637

Our Greek friends recommended we visit Margerites so we did. I bought a lot of pottery but they didn’t offer shipping nor could we find any place to ship it for us. I love all the pieces we bought, very special.
I ended up packing them in a a carry on, and was challenged at the airport check in. But I moved the pieces around and finally got on the plane with all of them. Hopefully there is now a shipping service in Crete.

Consider crowds.
Your visit it to the museum will be a couple hours. Then you will be within the window of time that Knossos will have tons of tourists. You then also may have a hard time parking. Best would be to do the museum the day before and the ruins as soon as they open.