On one hand, Youtube provides content in my native language, and a lot of stuff from Nico Nico gets Subtitled and transferred over to here.
However, from what has been brought over, I can see there is a lot more attention to quality.
But that's the thing. Only the quality things are being brought over, so all I see are the good things of Nico Nico, and both the good and the bad things of Youtube.
Beyond that, I think another edge Nico Nico has over Youtube is the laws in Japan regarding derivative works. It allows a lot more remixes and parodies than Youtube does.
Also many Japanese people want to go into Animation so by extension there is a LOT more animation coming from Nico Nico than from Youtube. Which is a plus side from me.
I would have to actually browse Nico Nico for several months before I would be able to make a final judgement (but can't since I only speak very very basic Japanese), so overall I think they are equal.