Choose this one by what you'll do in the water.
Under the surface, Egypt wins easily. The Red Sea has real coral reefs. Ras Muhammad National Park, about 40 minutes by road from Sharm El Sheikh or one to two hours by boat, has more than 220 kinds of coral and over a thousand species of fish. In Sharm and Marsa Alam the reefs run close to the shore, and some hotels have a reef you can swim to from their own jetty. Around Marsa Alam, Abu Dabbab bay is known for green turtles feeding on seagrass, and now and then a dugong. In Hurghada itself the town beaches are mostly sandy shallows and the good reefs are offshore, so you go by boat, for example to the Giftun islands. Bring reef shoes: sea urchins and stonefish live where you'd step.
On the beach, Crete wins. The Balos lagoon and Elafonisi, with its pink-tinged sand and shallow water you can wade across to the island, are two of the most famous beaches in Greece, and in 2026 Crete had 154 Blue Flag beaches, more than any other region of Greece. The sea is very clear, but it's the Mediterranean: rocks, sand and a few fish, not coral. Both are in the far west of the island, a long day from Heraklion, and very busy in July and August. Egypt's beaches are mostly hotel beaches, with a few well-known exceptions such as Abu Dabbab and Sharm El Luli near Marsa Alam and Ras Um Sid in Sharm.
Two safety notes for the Red Sea. Shark attacks are rare, but there have been deadly ones in recent years, including near Hurghada in June 2023 and near Marsa Alam in December 2024, the second outside the marked swimming area. And the UK Foreign Office warns that the safety of dive and excursion boats "varies considerably". In November 2024 a dive boat capsized off Marsa Alam, and in March 2025 a tourist submarine sank off Hurghada, killing six. Book boats through your hotel or a well-reviewed operator and check the life jackets.