Well in addition to Dominic's interpretation, it sounds kind of tricky if I don't know your intention. If you mean that you thought but were wrong that he has been there (unreal situation) then it's I thought you had been here before.... other wise it could be I thought you have been here before.

I thought (at a moment in the past) that you HAD been here before (earlier event in the past). The past perfect shows a completed action in the past that occurred before another event or moment in the past.

Thanks!

Had is correct. His presence there in the past happened before you thought about it. I think that Spanish and French also have past perfect and use similar methods thought=first event had been here=second event