Puerto Vallarta has a good bus system and taxis may be hailed almost anywhere. It's also possible to explore the city by foot although pretty expansive.
A variety of rental car companies have offices at the airport with rates from $450 pesos per day (US$29.75), including taxes.
Buses run throughout the city between the Hotel Zone, Marina Vallarta, Airport, south of Mismaloya and Boca de Tomatlan for 6.50 pesos, an affordable way to get about. Blue bus signs mark the bus stops.
Taxis are plentiful and inexpensive, but be sure to note the taxi's number and ask the rate before you get in as some are not metered.