I would go with Miami, but not by some huge margin. I don't subscribe to the "Miami is great, Indian Wells is crap" line of thinking however.
I'd also say that in terms of fitness these two tournaments are amongst the least demanding in women's tennis. Yes, they can both get quite hot but the same can be said about a great many outdoor events. The thing Miami and Indian Wells have going in their favour is that as two week tournaments players normally have a day off between matches. Playing 4 to 6 matches, which would mean for a seeded playing getting to the quarters or better, over a two week period isn't that demanding at all. Certainly not compared to the clay season when the girls have to play the Italian Open and Madrid back to back. Those events are 64 player draws, although as I understand it the Semi Finalists at the Italian will get a bye into the 2nd round of Madrid. Even so, that still means players face the possibility of 11 matches over two weeks on clay, a surface that tends to produce much longer more physically demanding matches. Now that is physically demanding.
Frankly there is no reason a player shouldn't physically be able to do well at both Indian Wells and Miami. It is the back to back one week events, especially those with six rounds that can be tough on a player fitnesswise.