There are two possibilities.

She might start wondering before you arrive, in which case I would say, If you are late she will be wondering where you are.

Alternatively, she might start wondering at the time you arrive, in which case I would say, If you are late, she will be wondering where you had been.

@LostInParadise right..

“Had been” involves time, possibly many positions during a certain time frame. Were, I think implies a specific fixed location, without necessarily any implication of time.

They are close, and essentially synonymous phrases.

@LostInParadise @Ltryptophan I wonder where did you get “had been” from? It was “have been” actually.

@Ticce it’s just conjugation. These are the same phrase.