I agree, "Teacher" is implied, but this translation, though accurate, perhaps much more accurate, than "Who's teaching you?" might be a bit confusing to someone who is just learning the language and should probably be introduced later on in the course.
I wonder how you should say :What do you study ? Co uczysz się OR czego się uczysz
As Kami12087 wrote, "Co studiujesz?", but it's when you do mean your university education.
"Czego się uczysz?" out of your two versions, but that's more like 'what are you learning right now'.