I think your focus should be on the content of the course rather than the minute points about their reputation (at the end of the day, reputation is only important to a certain point - and none of those three options are lacking in reputation, as you said). But with courses like history in particular, I imagine the courses can differ in terms of the modules which you have to take and the ones which you can choose. So you should choose the course which offers modules most in line with your interests - or, if you're not sure what your interests are yet (which is perfectly normal), then choose the course with the greatest diversity of topics.
The second most important thing is to choose a place where you'll be happy. You said each university has it's pros and cons, but which points are most important to you? For example, I would find it a positive that York has a collegiate system, but that might not be important to you.