think -- brain miss -- heart

You can say either but as David says "I miss you" is for when you are apart from each other. "I'm thinking of you" can have a less intimate meaning too. If you hear someone's brother died, or has been diagnosed with a serious disease, or they are just going through a difficult time for any reason you can say "I'm thinking of you" to indicate you know about their situation and care.

'I am thinking of you' has a more positive connotation. 'I miss you' typically means that someone is sad that the other person is not there, whereas if you are thinking of them you might be happy, but still care about them. I prefer to hear (and say) 'I am thinking of you' (although I might say 'I miss you' if it's true).