Both are actually a little incorrect. You could say either: I waited for you for an hour yesterday or I had waited for you for an hour yesterday You were just missing that one word "for" after "waited" in both sentences. They are both perfectly acceptable in everyday conversation between native speakers but the first one would be the more common way to say it.

The correct sentence is . I waited for you for an hour yesterday. Past perfect would need two actions in the past and one is clearly before the other. I waited for two hours but he had already left. (I started waiting at 3 but he had left at 1. He left before I waited). Please ask if you need more,