If the answer is "yes", so which one of the following is correct?
He is not indeed a wise man.
He is indeed not a wise man.
He indeed is not a wise man.
You can use indeed in a negative sentence. In an isolated sentence like this, "indeed" would more likely be in agreement to another's statement.
He isn't very wise
No, He indeed is not a wise man.
The first one sounds incorrect; the other two are correct, but with slightly different emphases.
He is indeed not a wise man
The emphasis is more on "not a wise man"
He indeed is not a wise man
The emphasis could be instead on "He"
The answer to your question is yes.
: truly <… their plan was indeed a risky one. — Lemony Snicket, The Austere Academy>
You may shift the adverb "indeed" modifying the verb is anywhere in and around the verb is which is negated by not to mean is not, and it won't change anything: all three will mean the same thing.
You start with...
He is a wise man.
Negate the truth of him being wise...
He is not a wise man.
Now, place emphasis on the fact he is not wise...
And the BEST of the three you present: "He is truly not a wise man."