If you're asking if we the player know, yes,it was Ocelot. I don't know who knows in the actual game universe. I can't remember what game it is, but I thought Ocelot made it clear at some point that he knew Boss was his mother. Maybe the end of Portable Ops? He doesn't know in Snake Eater.
EDIT: Spoiler tagged it, just in case.
Never played Portable Ops that might explain why I didn't know. So that rules out that possibility.