We are (again) for a long winterstay in Puerto vallarta and I can tell you it is safe there. That robbery took place in the mountains outside the city and could have happened in almost any place in the world.
Also realise nobody was hurt!
You can easily take a cab into Old Town, have a drink and meal at one of the beachrestaurants, walk The Malecon with many statues etc. will enjoy this too. If you book one of the city or other tours I am sure you will enjoy that. You will find nice shops near the port, but why stay there.
Thousands of people are staying here in hotels and condos, (apart from more coming by ship) all having a great time. Crime unfortunately is worldwide.
Bring Pesos, or take them from an ATM. You can bring US$, most shops will accept them but often against a poor exchange rate.
in Cabo the ship cannot dock, tenders will be used. If you book a tour booked on board they will tell you what time you need to take the tender or where the tour will meet/start.