I have not known you... Use "had not" to talk about a condition that existed in the past, but also ended in the past. When I left the company three years ago, I had not known you for very long, but I felt like I was going to miss you. (The situation existed and ended three years ago.) Use "have not" since you are talking about a condition that started in the past and still exists now in the present. I have not known you for a long time...(I didn't know your for long last week and I still don't know you very well now.) The condition of the relationship is the same now as it was in the past.

"Let's say I'm leaving my workplace and I want to say something..." So you use present tenses. You're talking about now. "I haven't known you for long, but I feel like I'm going to miss you!" The past simple and past perfect tenses are only for talking about the past. Past perfect is used to give a historical background for (which may include a reason for) the past simple action.

I haven't known you for a long time but I feel like I'm going to miss you.

And to answer your question: You would tell your co-worker when they're leaving, "I have not known you for a long time, but I feel like I'm going to miss you!" In a few years, when you're talking about when your co-worker left, you would say "I had not known you for a long time (when you left), but I felt like I was going to miss you!".

I know this isn't a very good explanation, but past perfect is a combination of present perfect and past simple. The 'have' changes from simple present to past simple while the 'perfect' verb stays the same. Does that help you understand it? This might be helpful: http://www.englishpage.com/verbpage/pastperfect.html