No, NW.js does not mean WebGL 2 is always supported. The support is the same as in the browser.
Why do you want to change the sampling mode, anyway? Normally a game's artwork style is suited to one or the other, and it seems unusual to offer both. Either it will look too blurry or too pixellated in one of the modes. There is no performance impact either way.
Because reasons ->
True that per se the sampling method has no (noticeable) impact on perfomance. However, as I might offer different raycasting resolutions (meaning rays cast in function of X resolution), I also might want to change the quality level at some point, as well as the sampling. This is somewhat indifferent to the art style at that point.
Sorry, I failed to specify that I use Chrome for C3 so I was under the impression / hope that the Chromium feature set is the same or similar and offers this.