I will have limited time in Crete and am going with a planned group. Debating going with group to see archaeological site at Phaistos and followed by a stop at Vori Ethnological Museum. Another option would be to take a day tour to Elafonísi Beach. This would be for early October and assume it still will be warm to swim.
I enjoyed both; I think it depends on your interests. I went to Elafonisi in July, and it didnt get warm enough to swim until around 1p. I found it very touristy, although it would be far less so in October. It was beautiful, and if it hadn't been so windy and cold, I might have been more in the mood to explore the island. As it was, we waded (to our waists) across the little channel to the island and set up there for the day behind a berm to block some of the wind. It was very crowded, although less so on the island. Phaistos was more interesting than I expected. Ironically (for this post) it was over 100 degrees when we went so we probably gave it short shrift, but I recall being glad we had made the effort to see it
If you took the trip to Phastos how do you propose the transportation logistics. Organized tour, private drivers, taxi, car rentals? Your answer will influence my suggestions for this day trip.
Perhaps also consider the other activities scheduled on your trip to build in a variety of experiences. We did both in our trip last June as part of a week in Crete. Elafonisi is not just a stretch of sand but has several different zones of pools, rock. etc. It has very large shallow areas that are sheltered from the open sea and therefore a great place to take younger kids or just wade. There is a big parking lot and the usual cadre of European beach umbrellas and lounge chairs with at least one bar/cafe and two sets of restrooms. But you can walk away from that area into 'unimproved' areas and see just natural beauty. It didn't appear pink, at least in bright sunlight. We were there 2nd week of June and found all spaces warm enough to swim arriving late morning. Comprises a large area so even when busy it didn't seem overwhelmed. Way down on the southwest 'corner' of Crete, so a significant part of your day may be getting there and back. We left mid-afternoon and stopped by a couple of the 'Chestnut villages' on the way back to Chania. I found those a little underwhelming so kind of wished we'd stopped instead at Milia, which piqued my interest.
Vori is very close to Phaistos. You can do both easily. In one day we stopped at Vori, Phaestos, Agia Triada and Gortyna, starting from Heraklion; we did keep moving and it was a longish day. I'm an ancient history geek but found Agia Triada a lesser version of Phaistos and skippable. We found the Vori Ethnological museum to be well-presented and of high quality; perhaps spent 1-2 hours there. We like museums that bring traditional ways to life. The museum consists of displayed artifacts grouped by function with good explanations. The less historically inclined might find it boring. We ate lunch at the Alekos Taverna in Vori which is less than a block from the Ethnological museum; DH and I were just remembering that meal and how it was simple but fantastic in a comfortable outdoor courtyard. Phaistos is in a striking setting on a promontory in the middle of a green and gold valley surrounded by purple-tinged hills/small mountains. We really enjoyed wandering around the site in the beautiful setting, following a guide book to the purpose of the various spaces. It doesn't feel like a repeat of the Knossos visit because the site is not nearly as restored. We make a point of getting into the countryside while on vacation and this area of Crete was perfect because it has a lot of activities to hold your interest but is also relaxing. The drive from Heraklion is easy on good roads, and driving in the area isn't difficult.
BTW we spent that night in Kamilari which was just minutes from Phaistos. It's a cute little hilltop village. We stayed at Xenonas apartments (traditional look with modern touches) and ate at Taverna Loggia just yards away. Taverna Loggia is one of those places where you are invited into the kitchen to pick out your dinner from all the wonderful things they have on the stove, in the oven and on the counters. The food and experience were amazing. I realize if you're with a group tour you may not have as many choices, but just adding this detail in case it's useful to someone else.