Professor Job Prospects for PhD in Computer Science vs Computational Neuroscience?
I will share my own results from my research as I am on the same boat (Torn between Bioinformatics/CS). From looking at profiles of recently appointed faculty across institutions, it certainly seems easier to get a position if you are a CS graduate.
Due to higher volumes of CS PhD's, most end up going in industry or doing post-docs for 1-2 yrs before getting a faculty position. Whereas grads from other disciplines (Computational neuroscience/bioinformatics) usually end up doing post-docs for a bit longer and I have rarely seen a recent faculty appointment in these areas without a post-doc. 
All reasons aside, It will greatly depend on your research/publications and to some degree the institution and your supervisor.