While I haven't done the tour in PV, I have done it in Costa Rica and it is a great experience. The canopy ride is south of the main part of PV and there is a lot to see there. You have two options. You can negotiate for a taxi to take you on tour for the day (costs about $100) and then you can do the tour and see quite a bit more while you are at it.
Or, you could rent a car for the day. Driving is reasonably sane in and around PV and again, there is a lot to see and do. You shouldn't have any p[roblems booking the tour directly with the company. You will also find numerous tour operators selling the tour at the cruise terminal's shopping area that might include transportation, as well.
Enjoy Puerto Vallarta