Remember that this game was built on nVidia and SquareEnix has already stated both in System Recommendations and on their site "Plays best on nVidia". There have been posted ATI conflicts in the past both by SE and by ATI regarding FFXI simply based on technological differences in the cards. These aren't necessary limitations no more than if the reverse were to occur on a game designed on ATI hardware. Of course SE does its best to ensure compatibility across many platforms, however inconsistencies in design, architecture, and just because of the sheer amount of manufacturers that can buy GPUs from ATI or nVidia and slap them on their circuit boards are always going to be an issue. These cards are both built on similar concepts to produce similar results, however they go about it differently and depending on your game, it may be interpreted best by one or the other.
If FFXI is your "main game", then yes, get nVidia. If you play many different games, it probably doesn't matter either way. You are going to get some games that seem to play a little better on one or the other.
*start sarcasm* Or just buy a video card from each vendor and switch them out as needed from game to game *end sarcasm*
Also, ATI manufacturers GPUs that even "value" circuit board manufacturers can get a hold of. This tends to happen when you buy the "same card" for half the price than if you got it from MSI or Asus.
With that said, go with well established companies that use high quality 6 layer circuit print boards and have long warranties because they back up their product. Asus, MSI, Gigabyte are a few examples. PNY is not a good example.
If you were just curious: I have an nVidiaEN7900 GTX / PCI-Express from Asus with 512MB DDR3.