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.
All Executive officials ultimately answer to the people. Indirectly, they all answer to the Congress, which Constitutionally has power superior to that of the President (as proven by their power to impeach him.)
The Constitution requires that the US be a republic. A republic is defined by the rule of law. Under the rule of law, everyone, even the king or the emperor is subject to the law, without exception. Therefore, a President can be indicted. This is not a debatable point.