I would've thought we were going to be #1 this week, and the Niners would be #2, since the Giants hung significantly more points on the Niners than the Patriots hung on us, but guess it didn't average out that way. I also am not real fond of yardage statistics being used for total defense. I do think stuff like Yards per Rush allowed is pertinent, but a lot of passing stats are inflated by the pass friendly rules in the NFL today, so I don't think all of them are always valid.
Giants only scored 3 more points on the Niners than the Pats scored on us. The Niners gave up a lot less yardage too.
Also, Chicago only has the best DVOA because they had a bye this week (I think).