I think they're pretty even in terms of DLC. FO3 had real clunkers in Anchorage and Mothership Zeta, but Point Lookout and The Pitt were outstanding. I didn't hate any of NV's (my favorites were Old World Blues and the Zion one), and liked how they were all related to the mythos surrounding your character and the world. Both games are incredible, but I prefer NV because it combined a morally bleak and relatively civilized world with meaningful choice and consequence. I also think Obsidian has the best writers of any studio today. Unfortunately NV was rushed by the publishers just like KOTOR 2 was - if they had a few more months to work on bugs and add the cut content that they intended, I think it would have been something very special.
FO3 just nailed the atmosphere and exploration of a post-apocalyptic world, though. I still don't like how utterly devoid of life the wasteland is in that game considering 200 years had passed, but it seems like they're fixing that in FO4.