I think that’s a great plan. Santorini is a must and Milos and Naxos are two islands that have both great beaches and lots to do and see away from the beach. Renting a car and exploring the interior villages of Naxos is a must-do and so is a boat tour around Milos. If you’re willing to cut Athens to 2 days, I would recommend Santorini 5 days, Milos 3 days, Naxos 3 days, and Athens 2 days.
Where to stay in Crete: A 300-year-old hamlet surrounded by olive groves, Kapsaliana Village Hotel exudes peaceful authenticity. On a sandy bay just beyond Chania, Ammos Hotel smartly combines Scandi chic with a child-friendly vibe. Blue Palace Resort & Spa beats the (stiff) competition in Elounda with its spiral stone Isola Beach Club, thalassotherapy spa, and boat trips to Spinalonga island, a national monument just across Mirabello Bay.
Yachts moor in the deep, sheltered harbour of Vathy, or Kioni, a miniature port where you’ll find Spavento, the perfect pier-side café-bar. Go any time of day or night for ice-cream sundaes, excellent cocktails, and a soundtrack to make your heart sing. Ideal for low-key family holidays or retreats, rugged little Ithaca is somewhere you can still disappear.