Y'know, I don't think it makes a difference. The subordinate clause is independent of the verb "wondering" and doesn't have to match verb tense. For example, all of these are fine:
I am thinking you have been to Europe.
I was thinking you have been to Europe.
I am thinking you had been to Europe.
I was thinking had been to Europe.
There is a subtle difference between "have ever been" and "had ever been". "Have been" implies "have the experience of", while "had been" implies "before a particular moment or event". However since "a particular event" could be "now", the meaning of both is very similar, at least in this context.
Also, there's often very little difference between "am wondering" and "was wondering". While you might reasonably think "was wondering" indicates a past event, in many cases the speaker simply means, "I was wondering this right before I spoke to you" -- in other words, up until this moment.
Additionally "I was wondering" is really more of a linguistic ornament used before a question or statement, and doesn't always mean that I was actually thinking about this for a significant amount of time. It's just a polite way to show interest.