I prefer fallout 3 because it feels much more brutal, and it is as if the characters are actually struggling to survive, that being said I do like the expanded crafting of fallout new Vegas and the weapon mods. What beats them both however is the playing fallout 3 using the fallout NV engine using tale of two wastelands mod.
Personally I prefer New Vegas to 3, simply because I played it before I played 3. I think 3 is a much grittier environment and as a result it feels much more post apocalyptic than NV, which is something that all fallouts should be characterised by. That struggle for existence. My other main gripe of 3 is that its is way more linear than NV, and that I would have loved to be part of the Enclave in 3.
Personally, I found the story of Fallout New Vegas to be a little better, as well as the combat system and additional side content... Which is odd seeing as I live in the DC metro area; you'd think Fallout 3 would be more nostalgic and relatable to me, but no.