I kind of stick to "post WCO" years, since Walsh and Montana, because the challenges and judging criteria changed so dramatically. Quarterbacks are now expected to complete around 65 percent of their passes and throws AT LEAST twice as many TDs and INTs. Nobody came remotely close to those numbers before.
There are guys who have defined the league since then: Montana, Marino, Young, Aikman, Elway, Favre, Brady, and Manning. Just outside of that are Warner and Brees. I fully expect Aaron Rodgers to be included fairly soon, maybe two more years. After three years, he's the highest rated passer in both regular season and playoffs... but needs to do it longer and preferably win something. It pains me, but Roethlisberger has already won two Super Bowls and has to be included in that conversation.
From those finalists, I would pull out Young (shorter career) and Aikman (wasn't asked to do as much) and Favre (played his team out of as many playoffs as into them, no Super Bowl for the last 12, 13 years of his career). I'd keep Montana, Marino, Elway, Brady, and Manning on that list, at least in my humble opinion.
From there? Really a matter of taste. Some remove Marino for never winning the Super Bowl... but I wouldn't.