POTUS can fire the head of the NSA. Truman fired Macarthur.
It's an interesting discussion the extent to which reality matches the law, but according to the US Constitution Obama is in command of the NSA.
The authority that the POTUS has over the NSA is more analogous to that of a CEO over a departmental division than that of a general over a battalion. As I said, the POTUS is responsible and accountable for the NSA, in the same way he is responsible and accountable for what our diplomats and ambassadors say to foreign governments, in the same way he is responsible and accountable if the FCC fails to secure network neutrality.
One of the more interesting consequences of this is that, if you were to place the USAF under the authority of the NSA, it would not violate the principle of civilian control of the military.
This is getting tiring.
Take a look at this list of former Directors of the NSA and count how many are ranking uniformed military officers. Spoiler: since the founding of the agency, all 17 of them.