Clearly, as previously stated, one has to ask: best for what type of paddling? Then on top of that, there is unlikely to ever be one "best", but rather a short list of "among the best".
That being said, for paddling in a combination of rough water (surf, high winds, confused seas, etc), I have found the Illusion by Sterlings Kayaks to be an amazing boat. It has tremendous rocker and phenomenal turning ability, yet still manages to track well, even without the "skeel". Speaking of "skeel", this is a brilliant design. It is a skeg, but it is located just aft of the paddler, which allows it to assist tracking in quartering seas and eliminate any weathercocking when desired, yet still allows good turning when deployed and does not stick out of the water when on steep waves. The kayak fits like a glove: deck height can be cut down to customize the fit, the seat is perfection, and I ordered it with a custom-fit bulkhead (rather than the SeaDog foot braces), which is absolutely worthwhile if you ever have that option. When paddling with steep beam seas or confused seas, the hull simply ignores them; just keep paddling. As to construction, with their high-suction infusion process, you get a very light yet very strong construction.
The bottom line is that this boat is like an extension of one's body, and is wonderfully transparent while paddling. By that, I mean that it just does whatever you want it to, such that you focus simply on the seas and your paddling, not the boat.
No doubt this boat belongs on the very shortest list of performance boats for rough waters. If you need more space for touring (for the Illusion, one would have to pack as a travel-light backpacker), there is the Grand Illusion, which shares many of the handling features, but with more volume. And they have recently come out with the Reflection, which looks to have even quicker turning, yet with novel front chines and more volume, to better serve those paddling large surf.
Prior to the Illusion, I paddled an NDK Explorer (with a custom Joe Greenley foam seat...same as the Illusion), and that is a wonderful, well-proven all-around paddler and competent tourer for any conditions.