If you're talking best possible gear, we think BM is pretty close to Survival in 3.3.3. Marks is ahead, and that's largely a function of armor pen, but again you are talking about absolute best gear. If you aren't in Icecrown 25 hard modes, then gear is likely to have just as much effect on your damage as spec. Ideally, things are balanced at all levels between level 1 and 80 with BiS gear, but there are going to be a lot of points along the way where that's probably not true. We see Survival hunters beat Marks hunters all the time in what I would categorize as average (meaning not server first guilds but capable of progressing) raids. Hopefully we'll see some BM guys up there too, but it may take higher gear levels.
I would be pretty surprised if guilds doing hard modes w/ access to lvl 80 BiS gear have hunters raiding as BM, or would be happy with a hunter choosing a spec that isn't min/max'd.
My suspicion is that the hunters with the gear you are describing will have a propensity to go Marks, because that currently yields the highest damage and raiders tend to play whatever does the highest damage. In a world without armor pen, that might not be the case (though I haven't done the math lately).
Nonetheless, it is also true today that Marks can beat Survival, and yet there are a lot of Survival hunters raiding. Our hope is that in 3.3.3 that there will be as many BM hunters as Survival raiding, which would be a really nice bump for BM. Maybe the estimates (ours and those I've read) about the boost BM is getting are overly optimistic. We'll see.
It's possible the Survival hunters are only going Survival for Replenishment, though all 3 hunters bring some pretty solid raid benefits these days.