I've had some weird squeaks/creaks come from the quick releases. Try taking them out and regreasing them. Also put a drop of oil in the cam.
I'll second the back wheel suggestion. If you can remove it and it goes away, that's telling.
But the more I think about it, I'll bet it has something to do with the quick release or the cassette. I'd have the cassette hub and quick releases regreased and reinstalled. When you're pushing hard and fast in a higher gear, that's where you'd get the most flex in both of those.
Of course, the another option is that you simply have a squeaky bearing in your rear hub. After pedaling away for a while, the grease warms up, thins out, and you get the squeak...