1989 hands down, no contest. Not just the best 49er team, but arguably the greatest team ever. #1 offense, #3 Defense. Should have gone 16-0. One of the losses was by 1 point. And if memory serves, I remember in the 4 point loss to Green Bay, there was an interception returned 90+ yards that got called back. That season Joe Montana set the record for highest QB rating (has since been broken), this is also the season Joe threw for nearly 458 yards on Monday night football.
In the Playoffs they obliterated their opponents. Beat Minnesota 41-13, then St Louis 30-3 in the NFC Championship, then Denver 55-10. Total domination.