Which one is correct grammatically? 

this two sentences are  both mean that you are a good doctor。

Both wrong.

You should say 你是个好大夫

But practically, we normally say 你真是个好大夫

Which one is correct grammatically?

"你是好大夫" is correct grammatically. 

So if want to say "you are a good doctor", it is "你是好大夫".

"很" means very, so if want to say "you are a very good doctor", it is "你是很好的大夫"；“好的” means "good", it is a adj