It is said that when Bill Clinton became president he said something like,
"First, I want to know who killed JFK and if aliens exist"
Considering that the intelligence community is so vast and operates under the concept of compartmentalization to keep secrets on a need to know basis -- is there one person or group (like a committee) that do know the truth regarding covert operations, assassinations, intelligence, etc.
I don't this is the best sub to ask this question unless you want historical examples of one person being completely in the know about what their intelligence agency was doing. But I think your question the way it's phrased is occupied with the present.
Stalin could be counted as someone or Joseph Fouché (head of Napoleons secret police), who were more in the knowing, but I think there was never, an all knowing person.
My argument is simply theoretical.
In the lower level of the pyramid, as you mentioned, there is compartmentalization.
The higher you go, the more you could know. But at the top level you have access to so much information, that you are phisically unable to look through them, all, so you prioritize, or others do it for you.
So, solely on a theoretical basis there can´t be an all knowing person.
Edit: I forgot an obvious one, J. Edgar Hoover, the first director of the FBI, from 1935 to 1972 (that includes, WWII, the red scare, the Kennedy assasination, Vietnam War protests, etc.) , who was seen as an all knowing person.