If you are staying in western or central Crete, the boat from Rethymno saves you the drive east to Heraklion before heading to Santorini. Rethymno is one of Crete's most attractive towns, with a Venetian castle above the sea and an old town of narrow lanes, and the ferry leaves only a short walk from all of it.
The service is simple: one company, Seajets, running a high-speed boat about twice a week between May and October. It makes the 76-nautical-mile crossing in about 2 hr 20 min and lands at Athinios, Santorini's main port. Outside those months there is nothing from Rethymno, and even in season the sailings are few, so the day of the week will shape your plans.
It is not a cheap crossing. One adult was listed from €104.70 and two adults from €209.40, and the monthly figures from last year sit at €104.70 to €109.70 a head. If price matters more than convenience, compare this with the Heraklion boats, where Blue Star Ferries runs a much cheaper conventional service all year.
Before you book, check whether the Seajets sailing falls on a day that works for you, and plan how you will get from Athinios to your hotel, since the port road is busy in summer. If you need a return, the same boat runs back to Rethymno on the same limited pattern.