For gaming and general desktop on Linux AMD is best if you want a dedicated GPU.
If you want a laptop with good battery life Intel is generally the way to go.
A lot of this is due to the enormous amount of effort Valve put into improving the open source AMD drivers, which is what is used on their Steam platform.
Of course if you want CUDA you need Nvidia, but if you use Nvidia to drive your Linux desktop expect some suffering to go along with it.