National lets you pick your vehicle if you sign up for their Emerald Club (its free). As was said above as well, Prius and other Hybrids are next to impossible to come upon. I worked in Car Rentals for two years and had spent time at 8 different locations across 6 cities and had only ever seen one for rental.
I would be more inclined to stay away from some of the companies like Dollar, Thrifty and Fox, as they may be a dollar or two cheaper sometimes, but can cause you tons of hassle at the time of rental or after. I tend to stick with one of the 'big boys' (Enterprise, National, Alamo, Hertz, Budget, Avis)