I would not say NYT publishes propaganda. They just truly believe their own opinion based on some ideology framework but confused their opinions with solid facts. So they see anything not align with their belief as a propaganda. In other words they seem to be against propaganda.
It's a meta-dishonest which is worse than dishonest which is a form of honest dishonest because many people trust meta-dishonest journalist. There are a lot of such kind of MSM journalists. Don Lemon for example.