If we're going to compare the Niners to the Pats, let me throw in another factor- division.
San Francisco did win a boatload of NFC West titles, but they didn't always run away and hide. The Rams pushed them at times and, at least through the Montana era, didn't always get swept. They oddly won more games at Candlestick than at Anaheim.
Atlanta was a division doormat more often than not, but every now and then (1983, 1988, 1991, 1993, 1995) they would spring a surprise.
New Orleans also made things tough at times with their defense and were seen as a worthy foil.
Compare that to the AFC East. Forget the QB play- Brady isn't exactly going up against Kevin Greene or the Dome Patrol linebackers twice a year every year.
During the SF 1981-1998 era, the 49ers had to sweat out their division here and there. New England only a few times has had to sweat out division titles- 2001, 2003, 2004, 2010. Outside of that, they basically have won their division in July.
Since the 3x in 4 years run, that division has gone WAY downhill.
The BUF/MIA/NYJ gap was way bigger than the old ATL/LA/NO gap.
The 49ers actually did surrender their division a few times (1985 Rams, 1991 Saints, 1996 Panthers, 1998 Falcons). Brady has failed to win his division ONE TIME while playing the full season.