Puerto Vallarta proper is an easy and inexpensive bus ride from the ship or you can pay $5 for a taxi. The Malecon is an interesting, sunny walk in front of beach-front luxury hotels and condos. For great views of Banderas Bay climb up to Casa Isabel for lunch.
Took a dusty ATV excursion an hour's drive north of town into a dry wash. Lots of off-road fun. You can walk all the way around the harbor and rent a kayak at the beachfront hotels to paddle your way across the channel to Lover's Beach or any of the snorkeling sites near there.
The free bus ride from the ship drops you off at the intense, northern end of Lopez Mateos, the main tourist drag in town, near Hussong's and other bars. The shopkeepers there work the sidewalk hard to hustle customers into their stores. For a more relaxed experience, skip the bus and walk toward the tall Marina hotel, at the southern end of Lopez Mateos. There is finer shopping and fine dining here with thinner crowds.