Puerto Vallarta. would be OK. The inner harbour is fairly big and has shops. There is access to the street out side and its a busy 4 lane to cross to Walmart. Side streets would still be pretty rough going in most areas once out side the Port.
When I was last in Mazatlan . The port itself was still pretty industrial and it was a ways to out side. I kinda doubt things are any better.
So as long as your ship has the ability to get you off and on PV would be OK as far as the information I have.
To add to what BSea said about Mazatlan, yes still industrial. Getting off and on the ship will not be a problem, the tourist area which is a large building with a courtyard and restaurant area lined with shops can get a bit crowded but still flat and accessible. At the far end of that area is a very large flea market style mercado filled with booths this area is also very crowded but again accessible.
Biggest issue will be getting from the ship to the shop area. Because it is a port with working docks passengers are transported to and from on trams and not allowed to walk on their own, at least the last time I was there a couple of years ago that's the way it was.
I would think that there would not be any problems with a wheelchair, a scooter might be a little more difficult.
Just outside the port compound there is no tourist venue at all, everything is miles away by taxi or tour bus. If you are interested in any tours in either of these ports the excursion desk on the ship can probably help you with best options.
You didn't mention the other port, Cabo san Lucas, so I assume you are aware that it is a tender port and may not have plans. I have seen people go ashore with wheelchairs but it is not a fun experience, at least not on and off the tender at the ship, in port not a problem. But the scooter would definitely be out.