<p>OP, you might want to take a look at NYU’s Tisch School’s Clive Davis Department of Recording Arts – they touch on several aspects of what you’re looking for, and are housed in the Tisch school right by the filmmakers, so there’d be opportunities for cross-pollination. Some of the profs are actively working on major scores as well.
However, I note that this program is not part of NYU’s school of music, so I’m not sure about the capabililty to pursue performance level flute simultaneously. FYI, I believe NYU also has an MFA program in commercial music (but I could be dreaming…)</p>