How to say How are you in Japanese

元気ですか? （げんきですか）？ How are you? (Lit. Are you in a good spirit, mood?)
はい、元気です。（げんきです） I'm fine, good. (It's not common to start complaining when someone already asked you. Instead, just say 元気です。

If you want to be really polite, you can say
おかげさまで、げんきです。 Thanks to you, I'm fine.
(Meaning roughly: You or your presence contributed to the fact that I'm feeling good.)

Please note:

It's very common to ask someone how they are in English without even caring how the person has really been doing or just to start conversation. In Japanese, however, you only want to ask that if you haven't seen the person for a while (at least a couple of days).