Crete is huge, Santorini is small. Chania is a very, very beautiful city, Fira is a very, very beautiful small town; they have completely different architecture. There are lots and lots of things to see in Crete and much fewer in Santorini (Akrotiri would be a must). Chania is still alive outside of the peak season while Santorini is almost dead. The view up from, or down into the caldera (Santorini) is simply stunning. Chania is certainly cheaper than Santorini. The bottom line is whichever you choose you'll be very happy you went there and at the same time disappointed you didn't go to the other. You'll immediately have to start planning the next visit to one of those two (or any of the 227 inhabited) islands in the Aegean and the Ionian seas.
