It depends on what you'd like to do. In many cases, you can easily get into and around town on your own. However, if you'd like to venture out, such as go up into the Sierra Madres, I'd recommend a ship tour to ensure you'll make it back before the ship leaves.
Check out our sister site, http://www.mexicoportreviews.com/
for some ideas as to what the ports offer.
I love this itinerary. Have a wonderful cruise!