Cabo is a tender port. Once you get to the tender pier, there are small shops at the pier, as well as many tour companies. You can walk into town (about a mile) or take a cab from there (hard to find a cab that is not a van though) for $3 per person. You can push a wheelchair into town as long as you can bump up and down a few curbs. Stay on the Esplande, not the street. Some shops are accessible, some require 1-3 steps to access. I know of no fully accessible tours there, although you might be able to get onto some of the boats that take people out whale watching or fishing.
In Puerto Vallarta you are about 3 miles from the main part of town where the Malecon and shops are. There are curb cuts but they are VERY steep and difficult to negotiate even with a pusher. The Malecon is not yet accessible, although there are plans to make it so. When we were last there in November last year, we used this company for a private tour with a wheelchair lift van, and they were very accomodating:
http://www.accesiblemexico.com/
In Mazatlan you dock in an industrial area about 8 miles from the Zona del Oro (main shopping and tourist area and the beach). You can take the accessible trolley on the pier to the gate of the pier area and catch a cab there. About $10-15 to get to the Zona del Oro. I know of no fully accessible tours there.