what to use had or had been?

“The patient had been died before doctor came”

is that a correct english…
or “the patient had died before doctor came” this one ?

The first sentence is wrong; it must be “the patient had died”.
“Had been” would be passive, but the verb “to die” is intransitive, it has no passive: I cannot *die you.

he patient had been dead before doctor came – whould be ok??

If you want to use “had been dead” I’d expect some duration of time: “the patient had been dead for two hours before the doctor came”. Moreover, perhaps “when” would sound somewhat better here than “before”.

“The patient was dead before the doctor came” is remotely possible, but it would be much more natural to say “the patient was dead when the doctor came”; that is because the word “before” implies that the patient was dead only before the doctor came, but was not dead anymore when the doctor was present.

Note that it should be the doctor in all of your sentences.