For one, I love the a6000. The built in wifi allows me to use my phone to operate it remotely, so I can just sit in my warm car and mess with settings and take shots. I can also offload photos with the wifi but at a low quality.
It is also much smaller and lighter. Overall a much nicer camera, and I'm sure would beat the nikon if you screwed on something like a $600 25mm f1.4 or 0.95 or something.
Just comparing body, and the nikon usually being $150, I'd say get a Nikon D700 instead of either, but second would be the a6000, or a6xxx family, depending on your other needs.
But my reasoning for the Nikon is I just spent 1/10th the cost I would with sony on an assortment of lenses, and I spent $32 on the camera body. The battery lasts about 1 year per charge as well. I didn't feel comfortable walking around by myself at 3am with $600 to replace in camera. if worst case I get robbed, I'm out $200 to replace or like $65 out of pocket. I was also going to mod it for astrophotography because I'm literally never going to use it during the day I think.