You need the present perfect continuous to place emphasis on the duration of the activity and the fact that it has continued into the present (your arrival). So, correct is:
How long have you been waiting for me?
A common, and shorter, way to ask the same question is:
Have you been waiting long?
This is a common misunderstanding. Your sentence mentions an action. That action seems to be in the past. The statement uses the present tense. Why?
Some verbs express action. Other verbs express state of being*. The verb "to have" expresses a state of being.
1) I saw the film.
2) I have seen the film.
3) I had seen the film.
In 1), the only verb is a past-tense action verb.
in 2), there are two verb words which form a single verb phrase. The "have" is a present-tense state-of-being verb. The "seen" is a verb without any tense but with the perfect aspect. This form does not express the action of the verb "to see". It expresses the result of that action.
I have seen the film. I possess a result of the action.
In 3), the "had" is a past-tense state-of-being verb.
The structure of 3) is rarely used on its own. Often, it's used to suggest that one thing is even further in the past than another:
4) I had seen the film when I read the book.
The action of "to read" is in the past. At the time of the action of "to read", my state of being included the result of the action of "to see". This suggests that that action of "to see" happened before the action of "to read".
_______________
* As far as I can tell, we use the phrase "state of being" because the word "condition" would be confusing. Verbs like "to be" and "to have" express a condition in the sense of "the way things are", rather than the sense of "something required for something else". We use the word "condition" in the second sense when discussing subordinate clauses, so we use "state of being" when discussing what a verb can express.
Best Answer
Had been wanting expresses a past event that is no longer occurring in the present, meaning you no longer want to meet the person.
Have been wanting expresses a past event that is still occurring in the present.
You would say:
You could replace wanting with longing, however, longing is more intense than wanting and may sound a little odd. It's not as common in everyday speech.