I often write
Article A was published in a paper which was non-reputable. [1]
However, I want to know if
Article A was published in a paper which is non-reputable. [2]
is grammatically correct. Also, does it sound natural?
Both are grammatical. If the paper is still "non-reputable" then by all means use "is". But if there is any doubt about whether it is still current, or is remote from anyone's current attentions then I would use "was".