Even though Bill's coaching legacy is diminished a little by Spygate - which he admitted was on him and I think will unfortunately cost him some votes for the HOF - I believe he is still the GOAT head coach. More rings than any other coach. Opposing fans and players cringed and many still do at the thought of facing a Belichick-led football team. When you get that kind of respect, you're an all time great.
Bill indeed is under .500 without Brady but I'm not penalizing him for that right now. Great players deserve way more credit for winning than coaches ever will. Great players can win with bad coaches - Peyton Manning took a .300 NCAA coach to a Super Bowl. Nuff said. The answer to the question was it Bill or Brady is, always was and always will be Brady.
But all time great coaches know how to maximize what they have no matter what and Bill has done that a lot more often than not, Super Bowl LII notwithstanding. I'd say he certainly did last year with a really bad roster on both sides of the ball, in 2016 losing the GOAT to suspension for a quarter of the season and in 2008 losing the GOAT for the season.