Commentaries have their place, as do Letters to the Editor, and would certainly be looked upon favorably by admission committees. They don't even need to be in Tier 1 journals. Anything published in a peer reviewed journal with you as an author should be listed on your application.
That being said, they are different than primary research articles and should be listed as such in your application. Do not write the citation on your application in such a way that it looks like a research paper. You should clearly state on your application that it is a commentary. This holds especially for big journals like Science, Nature, Cell, NEJM where an AdComm members or interviewers may have read the very issue you published in. I've heard a story about an applicant who listed a Letter to the Editor in NEJM on his application in such a way that it looked like a paper. His interviewer just happened to have a lot of back issues sitting around in the office and he pulled out the magazine to look up the paper during the interview. Needless to say, it was pretty uncomfortable when he found he saw that what was listed on this guy's application was not a full research paper but a half page Letter. So, include it on your app, but be honest and clear about what it is.