Here is some interesting arguments on both sides. Only you as a individual can decide.

The Case for…

Quite simply a cliche’ but lots of truth for it. “You can either hit the curve ball or you cannot. ”
Free Agency consistently depletes the team of some of their best talent along with valuable backups.
Why is this important ? Some will say that happens to everyone but here lies the cycle of life. In theory as a pro sports team, you are either up, down or the worst possible spot as a tweener. Well the Patriots are never down, or rarely have been. So the fact they are innovative on and off the field in systems including offense, defense , drafting and lower budget free agents that they sign makes it impressive that they have been this good this long. They quite simply make the most of their drafts, they do things unheard of such as moving guys on the offensive line in game and different weeks to different positions on the line. Brady rarely has the same target to throw to year in and year out. Some years they are standard double TE and some years they are a simple pro system. All of this and they never seem to run out of steam.

The Case Against

1Deflategate
2. Spygate
3 Spygate 2.
4. Pete Carroll has the best running back in the game on the goal line with almost no time left and he puts the ball in the air to claim victory. Of course we know what happened.

Take 1,2,and 3. I am supposed to believe that after being caught three times in different seasons, that these are all one off situations and are not going on all the time year in and year out ? That is laughable. One maybe, 2 I tend to lean towards not believing you, and 3 I most certainly cannot believe that this is not just standard protocol. Outside of Bounty gate which really is not breaking a total rule per se, where are all these teams getting busted for cheating ? No one is that I can recall so that makes it even worse that I am supposed to believe that three times was the only times, and it is not just status quo.

Pete would have won had he ran the ball on the last play.

The league rules protect quarterbacks and offenses more than ever now. I understand the idea to protect your stars, but the old guard and dynasties did not have that. Terry Bradhaw was 4-0 , called his own plays and got his bell run more than once, I do not think Aikman had earpieces yet, but he may have. Montana was not protected by all the modern rules limiting a defense. Also keep in mind modern football is played out of the shotgun, these guys would not know what to do if they had to walk to the line under center like a real man.

So you are 6-3 with major blemishes, and you cannot say they are not , because you cannot name any teams with these damn blemishes besides them. I am not saying you would not have won, but I am saying it is very easy to say maybe instead of 6-3. your record is 4-5. A team with a 4-5 record looks a lot different than a team with a 6-3 record. Now you can say that is too harsh, but look at it this way. if Pete runs, your record is 5-4, so now what I am suggesting is three known times you got CAUGHT were not the only times, simply the only times you got caught. So it is easily reasonable to point out that you got a SB at some point based on that rule breaking.
I am not advocating putting an asterisk or vacating like college ball, I think that is gay. I am saying your 6-3 and all those bandwagon people can easily be 4-5 and not so pretty.
And on a side note because the conversations intertwine, no Brady is not the GOAT. If Brady was 4-5 how can you say he was better than a Joe Montana ? Joe was undefeated, had no cheating and no rules to benefit the offenses the way they do today.