From a logistical standpoint, the three islands you mentioned are easily accessible by ferry from Santorini.
Most Greek islands have, as you put it, "quaint villages with small shops and nice cafes and restaurants, quintessential Greek towns with a relaxed atmosphere."
That said, you didn't mention why you picked these 3 islands in particular. I’m guessing it’s because they are among the top five most famous, crowded, and overhyped of the 21 Cyclades islands. This might actually contradict what you’re looking for. For instance, the Santorini you’ll be visiting is mostly packed with tourists and cruise ship passengers, so the vibe is far from relaxed.
Santorini receives 3.5 million visitors per year on an island with 30,000 permanent inhabitants.
Milos isn't really a "villages" island. Half of it is completely uninhabited and protected as a Natura 2000 zone. The other half has two main municipal areas: Adamantas (the port) and the capital, Chora, right next to it, plus Pollonia at the northern tip of the island.
So, beyond the social media hype, aside from the famous Sarakiniko beach and the Klima fishing houses—which you’ve probably seen a million times on Instagram and YouTube (and which likely influenced your choice?), Milos isn't the best place to find what you're looking for compared to other islands.
Personally, I would choose Naxos or Paros instead. However, with only a 3-night stay (which gives you just 2 full days), you won't have enough time to truly experience them, even if you rent a car.