The news site trialled the experiment for the first time on Saturday (27 July).
The move is part of the title's efforts to make comments more useful for readers, Marc Lavallee, a deputy editor of interactive news at the New York Times, told Journalism.co.uk.
The first story to try the new positioning of comments was an article about oranges and how the DNA of the fruit could be altered to resist disease. And as the story explored the contentious issue of genetically modified foods, there was plenty of reader reaction.
"For this story in particular, we knew many readers would arrive with fairly well-formed perspectives on GMOs [genetically modified organisms]," Lavallee explained by email.
He said that the news outlet "wanted to foster a conversation about readers' perspectives on the various factors informing their opinion" and "wanted to highlight the most insightful perspectives, especially for readers who don't normally wade into comments".
"We think it's a signal to commenters that if you're going to spend five, 10, 15 minutes contributing to a discussion on our site, we value your contribution and want other readers to gain from it."
The comments were elevated from below the line, placed alongside the story in a similar style to how New York Times's much-discussed Snowfall presentation uses pull quotes and and visual pointers alongside the main narrative.
The commenting experiment is "part of a broader effort to weave our digital storytelling – graphics, video, engagement, – into the narrative itself, instead of publishing them to different places on the web and making the reader to navigate between pages," Lavallee said.
"For comments, the trick is adding the right amount at the right time so that reader voice is elucidating and not distracting."
Other experiments showcasing reader reaction
The GM oranges story is the first to bring comments into the story in this way, but joins other experiments.
The New York Times has produced comment round-ups (like this one which outlines reactions to a story on dementia).
More recently it has incorporated the "reader voice alongside the narrative", Lavellee said, pointing out this story on urban migration in China featuring posts from the micro-blogging site Sina Weibo, which adds perspectives in Mandarin.
Another interesting example of experimentation is for this series on the high costs of medical procedures in the United States. The site displays responses to specific questions between chapters of the story, (plus there is an engaging interactive at the top of the article asking readers to guess what the cost of medical care during pregnancy).
"Stories take different shapes, so we're trying a handful of different approaches to find techniques that match, rather than looking for a single one-size-fits-all answer," Lavallee said.
So what has the reaction been to the various new positioning of comments? "We are happy with the results of this story and these experiments in general," Lavallee said. "Anecdotally, we've heard the same from readers as well."
"Given that we are selective in how we produce these pieces, most of our feedback is qualitative, but we've seen a few trends.
"First, we think asking guiding questions and showing examples of 'good' comments focuses and elevates the conversation overall.
"Second, giving readers more things they can interact with on a story, be they comments, slideshows, graphics, makes them more connected to the story overall."
Hat tip: Amy Harmon / Alastair Dant