Zack, just got back yesterday from the Sea Princess doing the same itinerary. We also did this itinirary in Oct 2000 on Royal Caribbean/Rhapsody, so I can offer two overviews.
On our first trip, we had never been to any of the ports, so we did totally the shore excursions. The city tours give a great overview of every place and offered lots of variety. We did the tequila/countryside tour in PV and had a blast.
I also must add in that we are not beach or water activity people, so that automatically nixed any of those tours.
On our trip this past week, we did a combo -- one shore excursion and two going on our own outings. For the second or third time visitor, this worked wonderfully.
Here is what we did in each port and how we booked it:
* Cabo San Lucas -- we did the glass bottom boat ride around the Lands End, Lover's Beach etc. On the ship, it was $29. Instead, we walked off the tender boat and booked it within 5 minutes of landing on the pier for $10 each. Great 40 min ride -- saw seals, great scenery and lots of fishes swimming under the boat. They will drop you at the beach or in downtown. It's also short enough that it does not eat up all your time in Cabo (we only had a half-day there.
* Mazatlan -- In 2000 we did the city tour. Neither of us cares for Mazatlan, so our goal was to get out of the city. We did the half-day colonial village/furniture making tour. Concordia is very quaint and picturesque. Had plenty of shopping stops mixed in, and it was nice to see the backwoods areas of Mazatlan. This we booked on the ship and paid $45 for a 6 hour tour. I would say we probably could not have done the trip much cheaper by booking a van for the half-day. By the way, you can book horse-back riding much cheaper at teh cruise terminal.
* Puerto Vallarta -- We love PV!!! In 2000, we did the tequila tour. This time, we went on our own and had a fab-o time. I used the guide from Fodors Mexico for a walking excursion. For $4 total, we were dropped by cab near the cathedral, we then headed several blocks to the Rio Cuale area. This is fantastic and not crowded at all. The river divides downtown, and so you walk down by the river and they have a whole shopping/restaurant area surrounded by beautiful shaded trees, lush tropical plants and so many singing birds. So relaxing, when compared to walking around downtown. From there, we made our way to Gringo Gulch (up a hill) to see Liz Taylor's old place (you can tour it for $8, but we were too cheap). Farther back into town, we peeked at the cathedral again, bought some cigs at a store and made our way to the malecon. Had a fantastic Mexican lunch at No Name Restaurant -- look for the Chicago Cubs symbol. Ask to sit on the 2nd floor. We waited 15 mins or so at another table until we could move to one on the edge overlooking the malecon, the artwork, and the gorgeous ocean. Truly wonderful. After checking out some of the statues along the malecon, we grabbed a yellow cab (another $4 trip ... be sure to ask ahead of time for rates) and headed back to the ship. It was a fantastic 5 to 6-hour outing.
Hope this all helps,