I think it depends on when you plan on traveling. We just returned from Portugal. I loved Obidos, but then part of it's charm was just sitting looking out over the green fields, wandering around the streets and the overall quietness of the place. There were just a few other individuals, enough to add a bit of a positive vibe, but no crowds. When crowed, I'm sure my opinion would be very different.
We had a car and also visited Alcobaca and Baltha. They are very different and I liked them both, so not sure how to rank them.
We had planned on visiting Tomar (which I was really excited to see), but they were experiencing a heat wave and I didn't feel like I could enjoy the place when too hot. I would rank Tomar partially based on the time of year, summer perhaps being a bit too warm.
We tried to see Nazare, but that was the one place where we did run across crowds. Parking seemed to much of a challenge, so we choose to skip it and spend our time at other less crowed beaches.