Last time I looked at either of them I found Ninject slightly better. But both have their drawbacks.
Ninject has a better fluent-configuration scheme. Unity seems to rely mostly on XML configuration. Ninject’s main drawback is that it requires you to reference Ninject.Core everywhere in your code to add [Inject] attributes.
If I may ask, why are you limiting your choices to these two? I think Castle.Windsor, Autofac and StructureMap are at least as good or better.