In general, they all perform adequately for normal usage.
PVC: Poly-vinyl chloride inner and outer with a fabric reinforcement in the middle; more inexpensive (didn't want to use the word "cheaper"), suitable for machine assembly (robotic welding.) Can be glued up by hand as well. Early problems with seams not staying together, plasticizers migrating out of the fabric.
Hypalon: An outer layer of hypalon, a fabric reinforcing layer, and an inner layer of neoprene. More costly than PVC per yard, how much varies with material weight. Has to be glued up by hand, as far as I know. Some problems with fading with long term direct sunlight, but generally holds up better than PVC for a given amount of exposure.
Polyurethane: construction similar to PVC; supposedly more abrasion resistant, but less puncture resistant (or so I've heard.) I believe it can be welded or glued. Don't really know that much about it. As far as I know there's one primary builder in the US using PU, and they're fairly high end (Wing Inflatables.)
As far as "best", it depends on what you need it to do, how you plan on caring for it, how much you can spend, and a bunch of other factors.