Most all are in a garage to the right of the terminal as you approach the airport (left as you are leaving).
As long as they are on-airport, they are effectively the same so I would balance cost and "reputation" of company as factors. I tend to book through AutoEurope and prefer the majors (Hertz/Avis/Europcar) as some of the bit players in Italy can be hit or miss but I have used an off-brand (GoldCar via AutoEurope in Pisa) once with no problems. My last rental that I returned to BLQ was with Europcar (VCE pick up).