Of the two, I would go with nVidia.
I'm not going to go into details about my personal preference for nVidia, nor type out the same stuff that's been typed already in other similar threads; but if you search the forums here a little bit, you can find a lot of very similar threads where the exact same question has been asked
People will always give both subjective, and objective answers to this sort of query. But if you love nVidia, then go for nVidia for sure. Yes, it works very well with Linux!