Crete, Santorini, and Naxos look quite doable within the 12-day block, but Crete’s beaches are scattered throughout a very LARGE island, Santorini really only has Kamari and Perissá (and some southern coast bays) and Naxos does have nice places to swim. If you choose only to visit those three islands in your relatively short time, you will do well.
Other factors, such as surface transport facilities and onward connections, will also affect the relative appeal of different airports and some long distance flights may need to operate from the one with the longest runway. For example, LaGuardia Airport is the preferred airport for most of Manhattan due to its proximity, while long-distance routes must use John F. Kennedy International Airport's longer runways.
Excellent choice of islands, though getting between them presents one or two challenges (they are not as conveniently connected like the Cycladic or Dodecanese islands so island hopping is not as popular in this island group). All three islands are served by airports with year-round connections to Athens and in the Summer with international charter flights from Europe. Let’s take the pros and cons of each island.
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