A year and a half ago, we were on Crete for 2 weeks, late September/early October. In the southeastern end, we stayed at the Terra Minoika Villas, owned by a former Mr. Greece bodybuilder. His on-site gym is open to guests, along with a beautiful location, but no pool, although the ocean is just down the hill. https://www.terraminoika.com/
A quick Internet search, though, says there’s a hotel with a pool in Kato Zakros. I’m not certain of its length, or suitability for laps, but you might check there.
Also on Crete, Sitia on the northeastern tip seems to have pools at hotels, and at homes that sleep 4. We stopped at the surprisingly good museum in Sitia, and saw lots of tourists toting pool toys and flotation devices as they walked to the beach while we drove thru town, but didn’t stay in Sitia, and didn’t check out lodging options. The Internet seems to show several with pools.
Crete was wonderful and varied, being a big, big island. Can’t give you any info on other Greek islands that might have pools for laps.