George and I were in Crete last June
We also stayed in Chania (Hania) it was on the water but not
Samaria Gorge is great, but its a hike of 5 hours and that is one way. Make sure you dont drive yourself as you would have the same hike back to get your car. If you like the unsual: Spinalonga is an island that used to be a leper colony. Its a 1/2 day trip You can also do a day trip to Santorini from Crete. The harbor at both Heraklion and Chania are worth the trip
We found going to the museum first was an excellent idea. It helped explain the ruins at Knossos so much better. Enjoy the planning!!