I'm not actually doing a music degree but I did think seriously about doing it for uni. You could just make a list of the good and bad points for each. Stuff I'd look at:
How much does the course fit your interests e.g. if you like theory/history/composing/performing/classical/jazz/etc, etc - how much option is there to do those things?
What are the music facilities like - practice rooms, etc
Does the uni have bands/orchestras/choirs that suit your style of music?
What is the campus like? Personally I have been to both and much preferred Leeds
Other activities/socieites etc that you might want to do like sport or other interests?
How easy/expensive is it to get to from where you live?
Which city do you prefer? Manchester is bigger so more gigs and other things going on, though Leeds still has a lot and is a great city too & easier to walk to places.
Look at unistats for how well rated the course is, student feedback, etc
Cost of accommodation.
If you've been to offer holder days or open days did you get a good feeling for the music departments, lecturers, etc. If you've emailed/phoned them, how helpful were they?
Those are the kind of things I would look at anyway. Good luck with your decision.