Where to publish a critical comment on an academic paper?
Do you know what is the best way to publish a critical comment on a paper published in top journal if that journal rejected the comment?


In another top journal. But your comment "have take a form of an independent paper" as Alexey wrote.

Check those two examples from Computer Science field. First (1) from ICSE, Software Engineering community top venue, where Monperrus offers a critical review on others' paper. Second (2), Arapakis et al. challenge the results reported in Bandari et al.

In my opinion, you should go for a peer-reviewed paper, which is a very noble form of scientific debate.