The first sentence can mean either 3 years have passed since you last met your boss, or you met your boss for the first time 3 years ago. It depends on context.
The second sentence means - you haven't met your boss for 3 years, but you may have met him several times prior to that (more than 3 years ago).
The third sentence means the opposite - you met your boss for the first time 3 years ago and [may] have met him many times since, but not before.
To avoid any ambiguity, maybe you should say either
It has been 3 years since I last met my boss.
I met my boss for the first time 3 years ago.