At least traditionally, a hand-written note would be considered better because it is seen as more personal. Of course, this is a matter of opinion and people may no longer see things this way nearly as much since email and other electronic communications are becoming more and more common.
A hand-written communication is generally seen as the most intimate form of communication. It is seen as less formal than a typed communication because it actually has your personal handwriting. It is not just a generic message that could have been typed by anyone.
The more personal message is better for a thank you note. This is because gratitude is supposed to be a personal emotion. When you want to tell someone you are thankful, it is best to do so in a way that shows that you care enough to give it a personal touch.