In the normal context where these sentences might appear, they are pretty close in meaning. If you're thinking of someone, you're probably missing them. If you're missing someone, you're probably thinking of them.1. I am thinking of you
2. I am missing you
However, it is certainly possible to say I am thinking of you in a somewhat different context and with a somewhat different meaning:
"Hello, Detective Smith? Yeah, this is Tony 'Slice-and-Dice' Garbonzo...you remember me, don't you? I'm the mafia hitman you sent to prison 15 years ago. Well, I just thought you'd like to know I got out of the joint last week, and I am thinking of you. I'm thinking of that pretty wife of yours, too. I know where she works. I know where your daughter goes to school, too. You can't be too careful these days, you know what I'm saying?"
Student or Learner