I think I have heard komentejo and komentaro used for the comment section below a blog post or a video.
Which of those words should I use? Is there a better word for it?
Both Komentejo and Komentaro are used, you're right. However, Komentejo specificly means "the comments' place", while komentaro means "large group of comments", refering more to the comments themselves than the section where there are posted. Komentejo seems better, since "en la komentejo" appears more concrete than "en la komentaro", where the whole of the comments needs to be seen as a metaphoric space in which you can enter. However you are totally free to use the one which seems the closest to your mind, or choose to build it by adding a synonym of -ejo, or whatever seems understandable, like komentsekcio, komentloko, komentbreto or even komentfalo, if you want to evoke a waterfall, for example. If you want to stick to the more used/understandable, Komentejo seems to be the best choice.