Cite the article, section and clause that prohibits it. There is one for members of Congress, but not one for the President.
There's nothing in the Constitution that even suggests a subordinate can't arrest and indict a "superior." If there were, the UCMJ would be Unconstitutional: It allows for exactly that. Look it up.
If Mueller can indict the Attorney General, he can indict the President. The same is true of any other Federal prosecutor. Federal prosecutors are Constitutional officers: They must be confirmed by the Senate:
[The President] shall have Power, by and with the Advice and Consent of the Senate, to make Treaties, provided two thirds of the Senators present concur; and he shall nominate, and by and with the Advice and Consent of the Senate, shall appoint Ambassadors, other public Ministers and Consuls, Judges of the supreme Court, and all other Officers of the United States, whose Appointments are not herein otherwise provided for, and which shall be established by Law: but the Congress may by Law vest the Appointment of such inferior Officers, as they think proper, in the President alone, in the Courts of Law, or in the Heads of Departments.
Note that not all Constitutional officers need be appointed by the President. Some can be appointed by other officials, even judges.
Such officials swear to uphold the Constitution; they do not swear to obey the President nor serve him instead of serving the country.
A Sitting President’s Amenability to Indictment and Criminal Prosecution [PDF]Date of Issuance: Monday, October 16, 2000
Headnotes: The indictment or crinminal prosecution of a sitting President would unconstitutionally undermine the capacity of the executive branch to perform its constitutionally assigned functions.
"The OLC memorandum concluded that all federal civil officers except the President are subject to indictment and criminal prosecution while still in office; the President is uniquely immune from such process...
Thus, in the absence of a specific textual provision withdrawing it, the President would enjoy absolute immunity.
The President is the symbolic head of the Nation. To wound him by a criminal proceeding is to hamstring the operation of the whole governmental apparatus, both in foreign and domestic affairs...
Under our developed constitutional order, the presidential election is the only national election, and there is no effective substitute for it. A criminal trial of a sitting President, however, would confer upon a jury of twelve the power, in effect, to overturn this national election."
Article II, Section 1, Clause 1 says that "the executive Power shall be vested in a President...".
So again I ask you, how does a subordinate prosecute his boss, the chief executive? Who does that subordinate answer to?
Again, the president can be impeached, convicted and removed, and then indicted.