Crete base cities, hotels and hike recommendations?

First off, Creteans are the friendlist folks I have ever come across. Be sure to accept any invitations that may come your way. The owner of the apartment I rented this year Mid-May asked all 4 of my group over to his house to hear him sing and play guitar with a spread of snacks and lots of homemade Raki and local wine. And I have found these folks very honest. Most places that have mid-high range hotels will be packed with tourists....especialy June - September. If you are going to lay down that type of cash for lodging, I suggest home or apartment rental in the smaller coastal towns. Unfortunately, I can not really help you much with pricey sleeps as I usually go the way of an apartment rental in shoulder or off season in these smaller towns, but you can look on Trip Advisor or Google towns you are interested in while looking at map for home or apartment rental. If you have not rented a car yet, I would suggest Anna Car Rental. Organise your days by region. You might want to rent in the Chania area for the first half of your trip and then rent in the Agios Nikolaos area for the last half of your trip, with the remaining last night close to the airport. Its a big island & lots to see. Most folks find 9 days still not enough to see it all.

Not sure if it's possible to avoid the crowds in late July. In the south, I like Sfakia a lot but it's a remote area. Matala will probably be overrun with tourists. On the north side Rethymno is really nice, and there are several places on the Akrotiri peninsula. Having a car will help a lot, you can cover the entire island in the time you have. Haven't been anywhere east of Iraklion so I can't speak about that...PM me if you want more info.