This paper does still count for your request, since it has an English language online version -
Novaya Gazeta from Russia. This is one of the trustworthy news sources from Russia. Most news outlets in Russia are state owned, but this one is a rare occurrence of the paper's staff controlling 51%. This, however, is not the reason why I find the paper trustworthy. It is a bit of a grim statistic, but Novaya Gazeta has
more journalists killed than any other news outlet in Russia. The majority of whom were either murdered by the state, or at least the state turned a blind eye to their death.
This next one is Russian-language only, and a radio station in Moscow. But it is a fairly good, unbiased news source. It's called
Echo Moskvy or
Echo of Moscow.
Unfortunately, one of the best English language news sources in Moscow,
The eXile,
closed its doors a few years ago. There are two possible reasons: one, that the paper was harassed into closing by the government. Or that the editor, Mark Ames, was tired and used some light harassment from the government as an excuse to close shop. Either way, it used to be a good source of insanely funny gonzo journalism with a constant streak of hard-hitting honest journalism.