Heraklion to Santorini is how most people join Crete to the Cyclades. Crete gives you mountains, gorges, Minoan history and a big, lively city; Santorini gives you the caldera, the cliff-top villages and the sunsets. Taking the boat north lets you do both in one trip without flying back via Athens, and Heraklion, with its international airport (HER), is an easy place to start.
The choice is between speed and price. The Seajets catamarans are the quick option, making the run in about an hour and a half on their fastest sailings, but they cost many times more than the conventional ships. Blue Star Ferries takes roughly three hours or a little more and was listed from just €15, with lounges, decks, restaurants and even cabins on board. Some sailings leave late at night, around midnight, which is when those cabins come into their own.
This is a proper open-sea passage of about 63 nautical miles, with no islands in between to shelter you. In July and August the meltemi wind can make the fast boats lively, so if you are prone to seasickness, the heavier ship is often the gentler ride. In exchange, a morning catamaran gets you to Santorini before 10:00 with the whole day ahead of you.
Think about the Santorini end before you book. All boats from Crete arrive at Athinios, the main port at the foot of the caldera cliffs, and in high season the single road up to Fira is congested when ships come in. Arrange a transfer or know which bus you will take, and book your Santorini room early in summer.
