You might consider exploring the east coast before or after Spinalonga, if you do you wont be dissapointed.
Can recomomend Faros apts in Xerokambos, and a stuningly beutiful sandy beach at the north end of the bay (the main beach is quite nice too but not for nudists as there is a tarmac road alongside it) , smallish, sandy bottom, good snorkelling and the few visitors that find it are usually Nudist. In the village there are 2 tavernas one which is especially nice.
Kato Zachros Palace apts further north offer superb accommadation with stunning views of the bay, mountains, and the palace ruins, if you enjoyed Knossos then you'll love it here and you have the choice of walking the gorge "valley of the dead" on your doorstep. Half a dozen or so Tavernas at Zakros, most offering excellant choice of food.
http://www.crete-today.com/accommodation/kato-zakros-palace-apartments-with-sea-viewA bit further north we stayed at
http://www.crete-today.com/accommodation/elia-studios-in-agathias-palaikastro these apts are on the edge of Angathia village and very peacefull. The owners father has one of the two tavernas in the village and you are assured of nice clean accommadation and good food failing that you are only 10 mins drive from palaikastro where because its a small town you would have more choice. The beach is only 5 mins drive from Elia apts.
Heading yet further north we personaly liked Itanos beach which is good for swimming and usually a few nudists at its northern end but space is very limited at that end. Just several hundred metres to the south is another beach which seems to have taken over by a local guy in that he has a bed and water supply thats ben piped down to a sandy enclosure with palm trees, there is a sign at this point saying "Nudist Beach" but whilst the beach itself is sandy there are many rocks once you get into the water. One should mention Vai beach which really is very nice but its commercialised, busy, and you have to pay to park unless you have a blue badge (wink) We did find that if you walked further along Vai beach it was possible to find shaded quite spot underneath one of the palm trees for which its famous for.
If it was my choice I'd base myself at Zakros and explore north and south from there. There is something special about the atmosphere at Zakros and if you stayed at The palace apts George would certainly look after you and allows all guests to pick fruit and veg from his adjacent garden.
Have a nice trip whatever you decide to do
