We did the Sierra Madre tour in January when we stopped in Mazatlan. This was a very interesting tour and you get outside of the port stops and get a chance to see a different side of Mexico. Very enjoyable.
There are lots of activities available in Puerto Vallarta. If you just want to wander there are some beautiful cobble stone streets and older homes in the hill above down town. There is also a very nice walk-way along the ocean in the down town area.
For a real experience in Puerto Vallarta, exit the port and walk out to the main road. Catch the bus here to ride into town. The buses are essentially old school buses. The cost is about 50 cents. The bus will drop you off in down town. If you want to go further south, there is another bus that will take you south to Mismaloya beach. Between these two bus rides, you will get a good over-view of the area.
An excellant company for tours in Puerto Vallarta is Vallarta Adventures. They have an english language web site. We have done both the mountain biking and also the canopy tour and enjoyed them both very much.
Enjoy your cruise.