I seem to get owned most by Sunbreakers.

I'm going to say only a few days after release of TTK that Sunbreaker has a strong super with range, which is awesome. Stormcallers have a strong super for smaller maps or game modes that force players to group up. Nightstalkers seem kind of meh right now, but that is just because players haven't gotten used to using the subclass or countering others with it. Two months from now, I imagine sunbreakers and stormcallers will still be strong in their respective ways, but nightstalkers will pull ahead in pvp again. They have so many tools to play around with, so when skilled players master the subclass, there will be many a montage posted on youtube.

Nightstalker will be the best. Once people get skilled with shadestep it will be obvious. And people will start posting threads about nerfing hunters again

Nightstalker but not by far... Storm caller and sunbreaker are a close 2nd and 3rd

In terms of super Sunbreaker is the best. However the abilities that the nightstalker has like cloaking melee and enhanced radar help you out more throughout the entire game. If you know how to use radar right then you the enhanced helps alot.

This is my UNeducated opinion (as I have yet to do Crucible since TTK released): I feel like on paper, the Nightstalker would do the best, as you can delete enemy supers, and remove their ability to move or aim or jump all with one shot. Also Shadowstep is fantastic for dodging rockets or snipers with. Also if you are in trouble, smokebomb shadowstep combo. But hey, like I said, that's just how I imagine the outcome based off statistics.