There's no single best PvP ship, but the current PvP metagame tends to focus around some of the heavier Medium ships like the Fer-de-Lance, Federal Assault Ship, and the Imperial Clipper*. They carry enough firepower to be dangerous to anyone, and have enough speed to dictate the range of engagements. Anything significantly tougher than them or more heavily armed can't keep up; anything else that can keep up is unlikely to really dent them, can't out-turn them that much, and will not hold up under their fire for long.
Of those three, the Fer-de-Lance is a strong shield-tank with good hardpoint placements and isn't really weak in any respects (except jump range and fuel tank size). The Federal Assault Ship has relatively weak shields but has enough internals to build a fearsome hull tank, and also has good hardpoint placement. The Imperial Clipper is the fastest of the lot and also makes a pretty strong hull tank, but its turn rate isn't the best and its hardpoint placement is poor for Fixed weapons.
There's PvP builds for just about everything; I've personally seen great use of Imperial Cutters, Federal Corvettes, Anacondas, Federal Dropships and Gunships, Imperial Couriers, Diamondback Scouts, Cobras (Mark 3 and Mark 4), Vipers (Mark 3 and Mark 4), and Pythons. I've seen video of even more things, including one memorable video of a T9 Heavy. However, the FAS, Clipper, and FDL are probably the three "best" that can handle just about any PvP situation.
*Yes, the Clipper is a Large-pad ship but it flies a hell of a lot like a medium, so I include it here.