Fallout 3 and NV are both great, each have advantages over the other in my opinion. The original 2 fallouts (not counting the ps2 game and tac *static*)...where also good, but I'm not a huge fan of strategy rpgs (still enjoyed them, but enjoyed 3/nv more).
Fallout 3 was the first fps rpg that really dragged me into the world (borederlands being another...but thats more fps and less rpg). I never got into skyrim (or the previous elder scrolls) nearly as much as Fallout.
NV was...probably...better in many ways, but it was also very similar to fallout 3 (almost like a very large expansion). That isn't a bad thing, and I still really enjoyed it (and have played through it at least 3 times), but it didn't have the freshness of Fallout 3 (which I have played through many more times).
I don't think it should be which one is better, they are both great, and hopefully fallout 4 is going to be the best yet. Wasn't impressed by fallout shelter personally...but it's free, and an ios game...so no biggie. I have not been so stocked for a game since Diablo 3....lets just hope this one isn't as much of a letdown!!