We love Puerto Vallarta. It's beautiful and rustic but organized and safe and enjoyable all at the same time. We took a white van into downtown and walked along the shops and beaches. We had lunch at Senior Frogs (don't recommend) and then grabbed a yellow cab back to Wal Mart by the ship. We then walked back to the pier.
We took the Colonial Villages of the Sierra Madras tour purchased through the ship. It was a 7 hour day on an air conditioned bus. The tour guide was knowledgeable but rather than talking mostly about the history of the land, people, etc. he talked mostly about himself, his beliefs and ideas. It was fine though. The tour was great and very informative (if you get motion sick take something because the road is very winding!)
Mazatlan is very run down and much less inviting than PV. We didn't have time for shopping after the tour despite that being advertised, people who wanted to get off and make their own way back to the ship (we still had 2 hours until sail away) were not permitted to.