I find that NYT comments accurately reflect the heavily liberal bias of NYT's reporting. Although I don't think that's wrong, I think there's room for constructive debate about the articles -- perhaps hosted on a different site.
Modern media do this every day already with their yellow-journalist hit pieces, biased comments to drive a narrative aren't even a skip away from that.
Then again, I would be shocked if PACs of all flavors didn't have pay groups of subscribers to crash the comments sections of the most prominent publications (NYT, WSJ, etc). Especially during the primaries last year. When you consider the amount of traffic they get, the top comment is valuable thought capital real estate during election season.