In short
By boat from Ierapetra's Venetian port, May to October (daily at peak). ~1h crossing, departure ~10:30-11:30, return ~16:00-17:00, so 4-5h on the island. ~€30-38 return. It is NOT doable in a day from Heraklion (2h30 to Ierapetra): you must sleep in the south-east.