'Why are you not sure?' is correct. Although depending on the context, it can sound a bit rude to ask this question. How were you wanting to use it?

It’s the second : ‘Why are you not sure ?’ This sounds rather formal and slightly patronising so it is usual to ask ‘Why aren’t you sure ?’ However this form is never used without the contraction ‘aren’t’ [as in your third] ; it would sound weird.