I also applied for a masters at the Madison program but will instead probably attend UC Davis, largely for financial reasons though I had a fabulous (and longer than expected) visit at Madison. Some, though not all the classes, were great and the professors were really awesome! Even the seminar I saw which I was told was the weakest wasn't bad at all. I also considered applying to the program you did at Brandeis but my advisor told me that one of her research colleagues on the faculty there did not recommend the program. I have no idea why, but perhaps it might be worth investigating what this may mean.
This is only a master's program, so what small advantage in prestige Brandeis has doesn't matter all that much. Both are good programs which could potentially serve as a stepping stone into an excellent (though not for sure Ivy League) PhD program. Even if you did graduate from Harvard with a PhD in musicology, there's no guarantee you'll not be poor for the rest of your life, so I'd say follow the money. If you decide sometime down the road you'd like a PhD in Gender Studies instead, Brandeis would keep your options open. The concept of a one-year MA, especially a joint MA, is kind of weird though and would probably have no real worth aside from helping you get into a PhD program, but it would cost half as much as a normal MA!
That's just my $0.02, but this is really for you to decide. Have you visited both schools? Do you know where you'd rather go if funding was equal?