I definitely vote for 2004 over 2005. More wins in 2005, even though they were upsets, and you just felt better about the team. I even remember a DVD I had hyping Brandon Lloyd, Alex Smith, and Frank Gore leading the next generation.
From what I'm told, 1978 was the nadir point for the franchise. The 1999 team was a team that just lost it's way without Steve Young, but there was still talent in the building. If I'm ranking top 3 worst, I'm going for
1. 2004 49ers- two wins in OT for a 2-14 team? They are inches away from being 0-16.
2. 1978 49ers- going off of what older fans have told me. I think the only guys that made the Super Bowl team were the O-linemen and Freddie Solomon.
3. 1999 49ers- Our current secondary is awful, and has been for some time in generating turnovers but if you TRULY want to see some bad DBs/pass defense, look no further than the 1999 49ers. I think they just gave up another TD. This is the team I think of when I question if we have the worst secondary.
4. 2015 49ers- A minor miracle this team won 5 games.
5. 2016 49ers- The team won two games, but for some reason, I took this a lot better than 2015. Or 2004. Maybe I was just numb to losing by this point.