4 night stay in Chania

Hotel Hera has IDEAL location... at the VERY END of Theotokopolou Street, the nearest lodging really to the street-end park, the parking area and the sea front. Of course it's not as upscale as Ammos. But I've stayed right across the street at Casa di Pietra , and right next door at Hotel Palazzo (not really a palace of course, just a very nice restored Venetian Manse, as are all of these). I am frankly shocked you have a choice of rooms on AUGUST 15!!! Are you aware that this is the BIGGEST holiday of the summer i Greece?? Combo of 4th of July, Memorial Day, Labor Day? ALL Greeks take off the week containing this Day (Assumption of VIrgin) altho like us, they "worship" at the beach or in the mountains.

In August thinking of hikng Samaria in heat of 95° or more is just wack. There are other gorges much less taxing. Look at Imbros Gorge.... below Rethymnon. rental car to top entry to gorge. 3-4 hour trek down at most (take walk-sticks!! you balance on rocks all the way). U can take picnic to stop & munchon way. At bottom, talk to waterside taverna where you can hire taxi to drive back up rim-road to your car. Unlike Samaria, no aches/pains next day.

Elafonisi once was a delightful undiscovered isolated beach. Now in high season (u must keep remembering you will be in HIGGGHHH season), it is daily overwhelmed until after 4 pm by HUGE Bus groups ... and when they depart, you are left with a very littered beach. I would think about Balos/Gramvousa instead. There are excursion boats for this -- depart from Kolumbari but I think if you buy a ticket in Chania, there's a bus shuttle for this.

OR -- with that rental car, you could go to FALASSARNA. The only beach in Crete that has a bit of surf -- as u know, the Med & Aegean do NOT have a tide -- but since it's open sea from Falassarna to SPAIN (!!!) the wind from west provides some surf. One year 2 friends & I had a great adventure. It started with , a couple nights in Chania, exploring old town etc, then got a car and drove west. (here's a map -- cllick &it gets huuuuge). http://www.explorecrete.com/crete-maps/images/Crete-eot.png

Between Kolmbari and Kissamou, there is a road that goes SOUTH, along the TOPOLIAN GORGE -- SO thrillling -- driver must keep eyes on Road!! Just around MILI somewhere, on the Clliff side of Road (RH) are stone steps leading up to Cave of St. Sophia -- the Orthodox dtried to "church it up" with ikons -- but its obviously a STONE-AGE place of Worship. Awesome. At ELON we turned west to coast & up to Falassarna, As map indicates a VERY scenic drive and NO tour busses ! We stayed a night at Hotel Petalida, on top of a bluff overlooking the beach. This family-run hotel is adorable -- it also has a restaurant overlooking the sunset, which is teh best seafood around, the family patriach runs a fishing boat. The best rooms are in separate building(s) across the small car-park ... little 1-story 2-unit affairs, with patios looking down on beach -- I have the most stunning sunset views of ALL from that patio. And the night's fish-soup was just as memorable.

Next day, we returned to the Big North Road and went east to Heraklion. There I recommend Hotel Kronos on harbor. Not as fancy-schmancy as boutique hotel Leto, but not as $$, and just as well situated. For evening, I recommend an "appetite walk" out the causeway to the GIANT Fortress. Returning, there's a "traffic circle right at the foot of the causeway, with several restaurants fronting on it. There's a glass-covered terraced one (O Psarri??? Maybe) it's an OUZERIE. That means entire menu is Mezedes. (Crete claims to be inventor of Mezedes-- like "tapas" only Greek). The 3 of use each got 3 mezedes, and indulged in gluttony!

You say that you have a long journey. If you have just completed a transatlantic flight then I would not recommend you try the Samaria Gorge the day after you arrive. That is a long hot and exhausting day and many people need the next day to recover.

I would suggest that you spend all 4 nights in Chania. It will take you at least a day to explore the Venetian harbour and the back alleys of the old town.
Chania http://www.flickr.com/photos/stanbr54/sets/72157632117917828/
Chania 2015 https://www.flickr.com/photos/stanbr54/sets/72157655164548880

If you want day trips Chania is still your best bet as a base for excursions.
The best way to visit Balos (which by the way is west of Chania) is to drive to Kissamos harbour and take the excursion boat. This gives you a stop at Gramovossa for the beach and a hike to the pirate fortress then on to Balos for the beach.
Elafonissi is a long day and will be very crowded. Better bet if you want beach time is to try Falasarna. It has some surf and is rocky, sandy and has an ancient site. It is only 15 minute drive west of Kissamos.

East of Chania is Ancient Aptera. It has 1800 years of civilization spread out over a mountaintop. That is a good 4 hour excursion. Be sure to find the arched roman cisterns, spooky.
https://www.flickr.com/photos/stanbr54/sets/72157632115757899/
Image 38 to 47 are Aptera and images 59 through 74 are Gramovossa and Balos excursion.

If you really want to leave Chania then I would suggest you head east to Rethymnon. It is similar to Chania and it has the wonderful intact Fortezza to explore. That also gets you half way to Heraklion for your night before the ferry. It is also a good day tyrip option from Chania.

Rethymnon https://www.flickr.com/photos/stanbr54/sets/72157654700502270

If you decid to stay in Rethymnon that will get you to Heraklion earlier the next day. That should give you time to wander central Heraklion with it Venetian era buildings and visit Knossos and the museum.
We stayed near the ferry port twice for the next day departure but last time stayed in the center of town. It was a short walk to the port (about three quarter of a kilometer) so it was an easy walk with our roll on suitcases. This allowed us to enjoy the center of town. Out at the ferry port it is kind of isolated and there is limited tavernas for you evening meal. Make sure you buy your ferry tickets as soon as you arrive in Greece because even in June our ferry was almost full.
Heraklion https://www.flickr.com/photos/stanbr54/sets/72157655935354556

I don't have the time to look up all of the hotels you have mentioned. For a hotel search I go to booking dot com punch in my dates and it will give you availability, price and even more important reviews.
I will give you my thoughts on where you will want your hotel to be. Look for Theotokopoulu street. It is a pedestrian only street just lined with hotels in every price range. There are also mini markets and shops. There is free parking at the foot of the street at the waterfront although there is fierce competition for spaces. Theo street is just a minute walk to the main harbour so it is close to all the action but just far enough away to be quiet at night. Any hotel on Theo street or in an ally off of it will be a great location.

We always stay at Pension Nora. It has all of your wants, is very well priced and over the past few years have added two little Cretan houses which have full kitchens and are quite delightful. Right across the alley is Jason Studios. While we have not stayed there I did visit it last year and have a friend who loves it.
Theotokopoulou St area http://www.flickr.com/photos/stanbr54/sets/72157632118491316/

We have also stayed at Vranas. It is in the center of the old town and used to be a Neoclassical mansion, It has now been turned into a studio hotel. It is a nice hotel but its location is noisier than Theo street.

Cross posting Janet. At least we recommended the same things

We spent 8 nights in Chania and it was just a tease. Four nights really is not enough time to split it with another area further east. Crete is a large island, almost a country unto itself and you need many days if not weeks to really experience it.

I would suggest staying in Chania for the 4 nights and wander around the Old Town, waterfront and areas out of the tourist zone such as the Splanzia District.

We stayed at Jason (Iason) Studios just off Theotokopolou Street and loved it. It's a budget accommodation with kitchenette, bed, table, chairs and a nice balcony overlooking a Venitian alley with lovely and colorful buildings.

You can do a day trip to Rethymno or to Palaiochora via bus.

Other than that you really don't have enough time to hike Samaria Gorge and enjoy what Chania is all about.

stanbr, this has got to stop! Our separate governments will begin to suspect a conspiracy!! Just basic agreement on Cretan joys -- nothing sinister!

We found a great place to stay via Airbnb, right in the heart of the old town. So much fun, walking distance to everything including a nice beach for the afternoon.
A day's rental car is a fine idea. Balos Beach, though, requires something of a rugged drive and rental companies will tell you it's not allowed. Thus, of the two I would probably just go to Elafonisi and enjoy the drive there and back.
One tip: Do not book a "tour" to Samaria Gorge. They charge a lot of money for those and you can just walk to the bus station in town and get a ride up to the top of the gorge with all the other backpackers. Cost about $10 RT plus boat ride at bottom as opposed to about $75 (if I recall correctly) for organized group tour.
Crete is huge with much to see. Couple days in Chania, beach day then gorge ought to do it. We spent one week in Crete and barely scratched the surface of the farthest one-fourth of the western part of the island.