The New York Times and The State Department are both putting their reputation (however much that means to you) on the line with their quotes, whereas WikiLeaks and its anonymous source, aren't putting anything on the line since a large part of their business model depends on making claims that can only be proven in their favor, but never in reverse.
Example, this claim about who is responsible for cutting Assange's internet access. Let's say the US did not cut his internet. There is absolutely nothing The State Department can say to make WikiLeaks supporters believe them. Whereas, anything WikiLeaks says about the US government will be eaten up by their supporters since the only people that can provide evidence to the contrary, WikiLeaks supporters don't trust. It's the same approach taken by Alex Jones (They want to take your guns, they want to put you in fema camps, etc...), Trump (A lot of people are saying...)
Oh and btw, I'm not saying you should just blindly believe what the government tells you, but until any actual evidence is provided to support another explanation, there is no reason to assume it is true.
Bonus hypocritical Trump tweet: https://twitter.com/realdonaldtrump/status/78183870603031347...