Not really breaking canon when Yoda tells Mace Windu "Always 2 there are, no more no less" at the end of The Phantom Menace. Which means at least some of the council are clearly aware of the Sith. Plus Ki-Adi-Mundi says this in front of Qui Gon and Obi Wan, possibly as a way to maintain the Jedi fiction that the Sith are extinct while the council is fully aware that they still exist in the shadows.