I went to Crete during the summer with friends and stayed a total of 5 nights. We picked Hersonissos as our base. It’s a resort town, about a 15 minute drive from where the airport and port are located, in the capital of Iraklion. We picked this spot because it was centrally located in the island and it also had a very lively night life to enjoy in the evenings, which was about a 5 minute drive from the hotel. Each day we ventured off to a different town and never ended up driving more then 1 ½ hours. Breaking up the 5 nights in Crete doesn’t seem practical because you end up loosing valuable town and dealing with the hassle of packing, unpacking, checking in and out.
We also ended up staying there because we fell in love with the all inclusive Hotel Arminda www.hotelarminda.com which offers a variety of activities in and around the hotels. Besides the beach behind it and the 2 pools on sight, you are able to go horse back riding, scuba diving, sailing and other water sport activities, as well as volleyball, tennis and it's just a great place to lounge around for some R&R.
Top towns to definitely see are Chania, Rethimno, Ayios Nikolaos and Iraklion. It seems you pretty much have all of the activities planned out. The only other options I would suggest would be to check out some of the many caves in Crete, I visited Diktean Andron which was very interesting and the drive was nice. We ended up stopping at several places along the way, far away from the tourist traps. You may also want to check out the Minoan ruins in Knossos.
As far as the best beach, I would suggest you take your swim suit and towels with you as you explore the island. You may find a place along the drive you want to stop for a quick swim. The beach behind the hotel I mentioned wasn’t bad at all.
Renting a moped is very adventurous, but not recommended unless you are a local. Some streets have no signs or traffic signals. It sounds fun, but I personally know of 4 different individuals who have had really bad accidents on mopeds in Greece. The best way to see the island and take the most advantage is by renting a car. If you are dead set on renting the mopeds, just stay to low traffic streets.
From Crete you can take a speed ferry to Santorini, which is about 2 hours. You may want to go to the port a couple of days before your trip to purchase the tickets as the schedules do change and purchasing the transfer way in advance is not necessary. Santorini is an amazing experience. There you will be able to lounge around and go to the different beaches. Red Beach is a must, and you will have to hike down a hill and through large rocks to get there. The beach is red due to the volcano and it has no sand but soft rocks and pebbles. You should also spend sometime at the Black Beach in Kamari in Santorini.
If you decide to go to Naxos, the beach at Plaka is suppose to be one of the top beaches in Greece.