I know what you mean about jobs, I talked to someone who worked in research they were offering a research position that was for someone who had a degree or a masters and they had all these post docs and people who'd just graduated from their PhD going for the position because there's no jobs out there for them. Its scary. Hopefully the recession will ease in a few years time and they will plough money back into research.
I have some input for your question however I am interested to know if you have a particular interest in an area of cognitive neuroscience. If so have you looked at what the respective uni's do in these areas? Or do you have more than one area of interest and you have things that interest you in both York's and Sheffield's programmes?
When choosing a uni course there are different things to think about:
What are the areas of study for each of the universities? Is there a particular area of cognitive neuroscience that you are interested in? If so which uni does the best research in this area (in terms of more interesting questions for you, just think if you do a PhD thats three years on one thing and you need to stay interested). If you do a good project for your masters then maybe that could be turned into a PhD.
What sort of environment do you like (in terms of the uni and the town)? When I was choosing a uni for my undergrad I went around the uni for a look and found the head of the course to be very friendly and this contributed to my choosing the course. Also some unis are stricter than others, I find I cope better when I am not told that I have to be in lectures.
At the time of choosing my neuroscience Masters I was interested in psychiatric disorders and possibly going into research within a pharmaceutical company, thus I choose the institute of psychiatry as a place to study.
Hope this helps good luck