Those are all very good schools - I don't think you can go wrong at any of them!
That being said, Illinois is (in my, and many others', opinion) definitely the best among them for Condensed Matter. They have 24 total faculty doing CM, including 11 (!!) theorists (in case it's not clear - that's a lot). They cover all aspects of CM, from topological materials to gauge/gravity to Quantum Info, from pure pencil/paper to computational/DFT based, and abstract field theory to very experiment driven. I'm not as familiar with their biophysics, but they have ~5 faculty listed as doing biophysics, which is more than most universities.
I actually have a few friends at BU doing CM as well. I'm not sure about their theory, but they have some very nice work going on in computational CM, especially in the ECE department (not sure if you're open to applying for ECE or not, but outside advising is always an option).
Boulder is a great program overall, but I've heard mixed things about their CM Theory. AMO is more their specialty, so unless you're interested in Quantum Information this may not be the best fit.
That being said, please don't just take my word for it; look at faculty webpages and at their publications to see what interests you. I'm speaking in generalities, and based on my experiences visiting. Hope this helps, in any case!