If I could, I would like to add another opinion than those given in the comments.
Since the second part of your sentence is not a complete sentence, you do not need a comma before the conjunction, but.
John does not help out but sits and plays games all day.
Sits and plays games all day is not a complete sentence. Therefore, no comma is needed.
However, rather interrupts the sentence and does need to be set apart by commas.
John does not help out but, rather, sits and plays games all day.
This would be the correct way of punctuating this sentence. In fact, the link given in the first comment seems to support this point. It says...
When a nonessential word or phrase occurs in the middle of a sentence, it should be set off with commas. EXAMPLE: Your work has been, frankly, awful.