We've done the itinerary twice, but on NCL Bliss and Carnival Panorama. In Cabo, first time we did a boat tour to Land's End and saw the arch. You can have the boat drop you off at Lover's Beach or Medano Beach and arrange for a pick up time. We had a short time in port, so didn't do this. Medano Beach has a lot of restaurants. No piers though, so you have to climb out of the boat and wade through the water. Second time, we did a UTV tour which was fun.
Puerto Vallarta, DH and I have been before years ago on a land trip. We really enjoyed walking around Old Town. First cruise, we did a taco tour. Guide was great and we got SO much food. Second one, we went to Las Caletas. DH and I had been there before and was looking forward to taking the kids. It's a beautiful place and so much to do (snorkeling, water slides, zip line for kids, animal experiences, etc). Things didn't quite work out though since we got torrential rain, lol. Kids still had fun though.
In Mazatlan, we did a Pulmonia tour. It was nice to see a bit of the city, but the driver tried to get us to go to a jewelry store. We were paying by the hour for the tour, so was not happy about that. Second time, we just stayed on the ship. Weather wise, it's a nice day for the water slides since the sea days can be a bit cold (we sailed in January and April).