We have been to Crete many times and stayed once in the East but mostly in the Western side.
We stayed in Plaka, a very small (blink and you miss it) fishing village around the bay from Elounda (about 10 mins on the bus). It was right opposite Spinalonga, you could get a small boat that took you to the Island for a fraction of the price the bigger boats charge, but without a guide. Take water with you, no toilets there and it gets very hot as there isnt much shade. Worth a visit. Elounda was very nice to visit, fairly quiet with nice restaurants and clean beach. AK Nik worth a visit too, as is the Lasithi Plateau with the windmills but we didnt like the south/East of the island much. We hated Rethymnon and Hersonissos - too busy like every city or big town, visited once and have never been back.
However, Chania as has been mentioned is well worth it, fabulous buildings and little lanes. Lots to see and the coast line is brilliant along there. Falasarna is one of our favourite beaches along with Elafonisos on the South West coast. Pretty villages along the routes. We stayed in Kolymbari where there is hardly anything there except a few restaurants, the beach isnt up to much with its pebbles so doesnt get busy but it is a good base to stay for visiting the area. Radvoucha is a lovely cove to visit with a tiny restaurant on its own by the beach. Dont bother with Kissimos, we felt it had no charm. We are not keen on visiting decaying ruins but love to walk and take in the views and smells of Greece and Crete has it all especially the West coast. A beautiful Island!