Why is Gibbs referred to a Gunny on NCIS?

Gibbs is not referred to as "Gunny" on NCIS. "Gunny" is a nickname for a Gunnery Sergeant in the United States Marine Corps.

Gibbs, while a former Marine, is a Special Agent in the Naval Criminal Investigative Service (NCIS), not a Marine.

It's possible you're mistaking him for another character, or you're thinking of the nickname "Pops" which is often used by NCIS agents to refer to Gibbs.