Big mods develop and evolve over months and years... FO3 has been around for a while, meaning, there more, bigger and more mature mods for it.
But, there are already thousands of good mods for FNV and because the two are so similar and, mod-wise, FNV is a continuation of FO3, porting mods from one to the other is doable and lots of modders develop for both games.
So... I guess I'm not being very helpful, but both are great.