Apple or Thinkpads, buying for department
I think that in most conferences/project meetings I attend, there isn't an overwhelming preference on one side or the other (I'm working in computer science, in case that matters). In other words, there are many academics happily working with linux, and many academics happily working with mac (some are even working with both), so in your case, there is no real wrong choice. 

From what I've experienced, in some places, there could be a preference for apple computers because of the way some universities order their hardware: if you ask for a PC, you might not be able to choose which one exactly, and you might end up with a low quality, cheap product, whereas if you ask for a mac, the quality is better (at least, that was true a while ago). But  I don't think it can explain why the proportion of apple laptops in the academic world is higher than that of the general population. 

In any case, I don't think that working within on environment will prevent the students to switch to another one later one if they need to.