hi there,
All the major rental companies are lined up inside the San Juan International Airport, as well as the airport in Vieques.
If you are headed to either Vieques or Culebra, though, you can either get a rental car and take a ferry over from
San Juan or Fajardo, or fly into the islands directly and pick up a car there. It's about the same, pricewise, though most prefer the convenience of doing everything out of San Juan.
Other major cities like Rincon and Ponce are also excellent places to pick up a rental car in Puerto Rico.
Regarding public
transportation, Puerto Rico transport is cheap and comprehensive with great service.