In a world of infinite choices, I believe that making deliberate choices is a good exercise, whether you do it via a strict whitelist/blacklist domain filter or some other means.
Many times, I don't actually read the article and just read some of the comments. Instead of filtering by the domain where the article is hosted, I use the title and its underlying theme or subject as the filter for which article comments I will read. I'm not interested in every single subject posted on HN so I just look for the subjects that I am interested in. Reading the actual article can take time. For me, I find skimming some of the discussion in the comments as a quick proxy on what the article is actually saying or the value of the article.
With all filtering, there is always the risk of false negatives where you skip something that you would have found of value or really interesting.
I agree that some of the most interesting articles are from non-mainstream sources. For example, the recent article about weaving.