The first one means just that Sarah has been to Tokyo, some unspecified time in the past (and it probably has some present consequences). The second one stresses that Sarah had been to Tokyo prior to something important in time line.
Let us try to contextualize them:
- I need a volunteer with some Asia traveling experience, any suggestions?
- Sarah has (already) been to Tokyo.
- Oh, really? Have you already been to Tokyo Sarah? When?
In the context above, one cannot use "had been" instead of "have been".
- Mark, did you get the promotion?
- No, unfortunetelly not. The boss promoted only Sarah, since she volunteered today for his new Asia project.
- Why didn't you volunteer? You are going to Tokyo next month.
- Well, Sarah had (already) been to Tokyo.
In this last situation, since Mark is talking about a past situation which happened in his work, Sarah's being to Tokyo became kind of a "past of the past", so the past perfect tense is used.
PS Not a native speaker
Student or Learner