If you are talking about the photograph or some words on a magazine front cover, you might say "on" but you would be more likely to specify "I have seen it on the cover of a magazine".
If you are talking about another object which was sitting on top of a magazine, you might say "I have seen a coffee cup on a magazine".
Note that without context it's hard to tell whether "I have seen" is correct here. "I saw it in a magazine" sounds much more likely to me.
- For Teachers