There isn’t really a difference between these two. “Gonna” is slang for “going to,” so “i’m gonna miss you” is also “i’m going to miss you.” “ Going to” and “will” are both in the future tense, and they have very similar meanings. The only little difference I could think of is that “gonna” is less formal than “will” because it is slang.

In my understanding I miss you means you are missing someone now. And I'm gonna miss you means. When I am away from you, I am going to miss you. So I indicate future.