Both are very reputable universities, I wouldn't base your decision on that.
The Edinburgh course will probably give you an edge in PhD applications, especially somewhere like Columbia, due to the longer research project. This advantage comes in the form of exposure to a more comprehensive project (e.g. more techniques), so I wouldn't say going for Imperial would severely impact your chances of admissions. However, the Imperial course being an MSc might limit your opportunities in terms of joining conferences etc.
Have you considered the labs you could join at either institution? What are the lecture courses that you can take to complement what you've learned in your undergraduate? Do you have a preference as to where you want to live?