You seem to have done your research quite well. Your list of options are all good choices in west Crete.
I would eliminate Elafonissi because it is likely going to be a destination when you visit Chania.
Logistics are important so can you tell us when you want to add the two days at the beginning of the trip, middle or adding on at the end of the trip.
Your decision may be important to get back to the area near your airport or ferry port for your departure from Crete.
Anyway I would be tempted to go to Sougia. Its a delightful village and the drive over the white mountains is amazing. Sougia is pretty laid back and as you have noted you can take the ferry to do the Samaria gorge from the bottom which is less strenuous than doing it from the top.
The ferry trip along the coast is beautiful.
Just a suggestion, the entrance to the gorge is 3 km from the ferry dock. If you plan to walk it that adds 6 KM to the hike. You may want to find the service that provides transport to the gate and from the gate.
One problem at Sougia is there are not a lot of hotels so you need to find accommodation now.
Here are some images of Sougia and the ferry trip.
Samaria Gorge the easy way.
https://www.flickr.com/photos/stanbr54/albums/72157670610409530/
Sougia
https://www.flickr.com/photos/stanbr54/albums/72157696633322660/
