Many of the articles on India are negative. However, bad news sells. So, I wouldn't have expected anything different. There were some general non-negative articles (Whales dying on shores, LGBT laws gaining momentum). There was an absence of positive articles about India from a quick search.
By contrast, I looked at Australia in the New York Times. Most of the articles were on sport and bushfires, so, there's definitely a different focus and attitude. Australia seems to be social events, India social unrest and injustices.
I consider the New York Times to be prejudiced at times though. However, the article in question was well written, despite a lack of explanation of why there are less women in the Indian workforce than there were in the past. One example of NYT prejudice I remember was about Australia's first female PM, Julia Gillard. The NYT described Australians (collectively) as misogynistic because we dared to criticise a female Prime Minister about her looks. I searched at the time and found ONE media reference to a criticism from Germaine Greer - a prominent feminist - about Gillard's fat ass (I saw 'ditch the witch' after this article). I contrasted this to other PMs: John Howard in a bondage pose with his nose up George Bush's ass among many personal attacks on him (conveniently ignored), tony Abbott in his budgie smugglers and exaggerated lips, etc. The NYT must have had very big blinkers (or my prejudice comment holds).
The reality is that India does bad things AND the media is very prejudiced. I think the dismissal of prejudice in the media is dangerous.
Maybe, a letter to NYT suggesting some positive things in India may help raise awareness.