They can both be used the same way, but in everyday English:

How have you been is a real question. Expect a real answer if you ask this.

You: Hey, how have you been?

Friend: Great! I just got a promotion at work, so I've been really busy.

How are you is often just another way to say hello. You can say this when passing an acquaintance or co-worker on the street. The answer is typically, "not bad." Don't expect many details in the person's answer.

You: Hey, how are ya?

Some guy: Not bad. See you at work.