I just checked the video, it was Sam who said he feels like it's the least popular GTA (in terms of impact), not DJ. DJ was confused himself when Sam said it. Though DJ did go on to say that he thinks it's probably the least popular among 3, Vice City, and San Andreas.
Which I still very much disagree with, it's the best selling game of the three, and was the best selling game of 2004, beating Halo 2 by almost a million units in the US alone.
And that's not even getting into the cultural impact of the Hot Coffee fiasco, almost getting an AO rating, spawning goofy lawsuits and political outcry, all the memes about Big Smoke / "Ah shit, here we go again," etc.