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You can take a ferry. They're nice. You'll stop at Santorini on the way. But the ferries go out of Heraklion and most people stay in Chania. There's an airport in Chania but when we did it there weren't any flights from Chania to naros paxos You have to go through Athens in which case the ferry may be quicker.
We did ferries between a number of Greek islands. We used ferry hopper to see all the options and there are high speed ferries (we were on the seajets) that make the trips pretty quick.