BM is still on top, especially in arena, but even in BGs. Dealing with Line Of Sight issues is a lot easier with BM - you can keep pressure up both while people LoS you, and while you are LoSing others when necessary. MM is viable with certain team compositions, but it's not that great.
5.4 will be interesting to see what happens as ONLY MM will retain Silencing Shot (as a baseline spell for the specialization). In my opinion BM will still have a place because of the LoS/kiting, spirit beast heal utility and mostly for the "free trinket" via Bestial Wrath.
Survival is the weakest spec currently, but in the right situation can be good for BGs insomuch as it brings decent overall pressure similar to a Boomkin or Lock albeit probably not quite as good as those classes.
Best bet when playing hunter either in arena or BGs - take along a Disc Priest or Resto Druid.