It's hard to say which team is better at the moment. Things like 'common opponents' only tell a partial story.
For instance, the 49ers played the Rams without Matthews and Gurley. Gurley hasn't looked great this year, but he's absolutely vital to their offense which is an area the Rams struggled in yesterdays game. The key take away from that game (IMO) is how well the Ram's defense contained the 49er's offense despite losing the TOP battle by 18 minutes. The Rams boast the 25th best defense in the league. That's the second best defense the 49ers have played behind Pittsburgh at 13.
Seattle hasn't looked great in the 'common opponents' department, but the circumstances leading into those games were very different. One thing to consider, both Seattle and San Fran have played easy schedules thus far. That trend continues for San Fran, they have the 20th ranked schedule rest of season. Seattle, on the other hand, has the toughest schedule rest of season.