Cabo is our least favorite port and Cabo Wabo is definately just a tourist trap. We went there on our first trip and felt like we wasted time going there. Then again, some say that about The Office and we love to eat there! Or just up the hill is Baja brewing that has excellent food and view of the whole area.
In PV you could go to the Malecon, but if you been before, maybe try the marina. It's closer to the cruise ship. We did see the famous crocodile on our last trip (it's huge) and we weren't planning to eat there, but we got talked into eating at one from the vendor promoting his restaurant and it turned out to be excellent and one of our favorite meals.
Haven't been to Mazatlan in years, but we will be there in April. We're probably going to Stone Island in the AM and walk around town in the afternoon.