Here's a link to a pretty good article on ESPN about the Niners run game so far this season. It's insider protected so if you have insider go check it out.
For those without insider here is a quick summary
The Niners are getting a lot more with the players they have. They state that San Francisco hasn't added to much to the offensive side of the ball (that's up for debate in my mind. The 9ers have added several weapons and upgraded the right guard position). They attribute most of the gain to the coaching staff (which we can all agree is excellent, maybe the best in the league)
Basically the Niners have the best run blocking offensive line in the league and it's not even close. The unit is ranked 1st in ALY (adjusted line yards; which is basically the amount of rushing yards that can be attributed to the offensive line). San Francisco is currently average 5.34 ALY the next best team is Seattle (BOOO we can all agreee they suck) at 4.76 ALY. And only two teams, 2000 Rams and 2002 Broncos, in the last 20 years have finished above 5 ALY.
On top of leading the league in ALY, SF also average 6.1 yards per carry which is tops in the NFL and 2nd in % of first down runs (defined by gaining more than 4 yard on 1st down, 6 yard on 2nd down and 10 yards on 3rd down. I'm not completely sure about those numbers but its something close to that maybe somebody could clarify.)
That's the jist of the article hope you guys enjoyed.