As of right now epic gems will come from random drops in dungeons.http://www.tentonhammer.com/wow/patch43/epic-gems
"L: Will we be seeing epic gems in 4.3?
GS: Great question, and yes, you will! The way we're hoping to set it up, and we kind of have this working but things could change before we go live, is when you kill a boss on normal or heroic mode, each player gets a geode, and when they open the geode there's a chance they may find an epic gem inside. If not, it'll have blue gems or something like that. We really want it to feel like an individual reward, and not something that the raid leader gets to have fun in deciding who gets the gems, or they all go to the guild bank or something. We really want it to feel like an individual reward.
They'll be somewhat rare. It may take the entire content cycle before someone has replaced every red gem they have, but they won't be so rare that you won't see them.
L: How is that going to work with profession bonuses? Blacksmithing with its extra sockets, assuming that you could get ahold of a full set of epic gems, seems like it would all of a sudden become the best profession.
GS: I think the epic gems are like 10 stat points over the current ones, so it's a nice boost, but hopefully it won't push everyone towards Blacksmithing.
Not from pyrite.
But I am making a killing in ebonsteel belt buckles, selling pyrite bars, and prospecting for gems.
Trust me when 4.3 drops you will want all that pyrite...if you have a maxed out blacksmith.