> So, my question is: To a native speaker, which one/ones seems/seem
> correct.

This non-native speaker thinks the sentence sounds just fine. The correct (and only possible) interpretation is number 2. I'd drop the accent though : *I don't like these comments coming from you (of all people).*
Also, it is not a gerund and it is not a phrase. "These comments coming from you" is only an auxiliary short of being a full-blown, finite clause. 
Grammatically speaking this ing clause is a catenative complement of the verb "like" . It is not uncommon at all for the ing clause to have an overt subject as in your sentence. Unlike catenative sentences involving to-infinitivals, the NP that comes in between the two verbs in partcipial catenatives is never understood as the (semantic or syntactic) object of the matrix verb. 

I think that "these" in "these comments" 
 stands in the way of interpretation 1. If you drop it, the first interpretation works and the second one doesn't. (at least how I read it at this moment, I may change my mind). There could be ambiguity in this construction, for example:

> I don't like people coming to this place.