Article I, Section 8 grants Congress to make all laws it deems necessary and proper to regulate and organize the navy, and land forces of the United States. If the Congress wanted to, it could pass a bill tomorrow abolishing the CIA, FBI, and the entire military. The President has NO authority to disregard Congress' laws. Indeed, the CIA and FBI are creatures of Statute -- the scope of their duties, who reports to whom, what reports ought be made, etc., etc. is entirely up to Congress.
I don't see the words intelligence agency in there. Aside from that, the point is, Congress can set up agencies, but it is up to the Executive Branch to run them. But we've already progressed well beyond that point in the debate - it really comes down to the nature of the change in the law being spun as something else by the media.