We flew into Iraklio, rented a car, and drove to Kalives (near Hania). The national road is good and makes for fairly speedy travel.
Kalives is a lovely town -- small and uncrowded, on a beautiful beach, yet developed enough to have a modern supermarket and a good assortment of restaurants. We stayed in an apartment at the Ismini Apartments (http://www.greekhotel.com/crete/chania/ismini/home.htm). The Ismini Apartments were very nice. Ismini is an older woman who is very friendly and keeps beautiful gardens. The pictures on the web site are absolutely accurate -- the beach is just across the lawn. The beach right in front of the apartments is next to an outlet of cold spring water, and a very short walk around the breakwater takes you to the main beach where the water is warmer. The benefit is that the beach right in front has few people on it. The only negative to the Ismini Apartments is that they are on the Kalives town road and get some road noise -- mostly from motorcycles. It's not terrible -- I used earplugs at night and got used to it during the day. I happily recommend the Ismini Apartments.
For food in Kalives, go to Zorba's in the town square.
Hania is attractive but solely a tourist trap, and can easily be skipped.
We then drove to the south shore of Crete and stayed outside of Kamilari at the Ambeliotissa Apartments (http://www.ambeliotissa.com/). These are nice as well, and there is a new, small above-ground pool. The property is especially oriented to families with small children. The property is set amongst olive groves, and is down a steep hill from the very small town of Kamilari. It is a mile or so to the beach town of Kalamaki, a small and lovely beach resort. For food in Kalamaki, I recommend Aristidis (at the northern end, not to be confused with Taverna Giorgos Aristides at the southern end, which served cold frozen pizza).
We also visited the ruins of the Palace at Knossos which, sadly, I found underwhelming.
Crete makes for a lovely beach vacation. Going in June, we found places that were not crowded as I had feared. The sun is extremely hot during the middle of the day, but it is dry heat and pleasant in the shade. The only negative was the car rental -- we used "Motor Club," which has no counter at the Iraklion airport and no-showed at the drop-off time, leading to panic and problems that no one wants. Use a car rental that has an on-site counter.