I have to admit, pretty much every final boss track is wonderful. I haven't ever been disappointed, even with PC-98.
However, as the specification is stage 6 boss, that rules out a few games by itself. Plus, for me, it takes Border of Life down a notch or three, because that's two separate themes and they only work best together.
And like a lot of people, I think the instrumentation in 6 keeps it from being awesome, although it's still damn good.
I'm going with Cosmic Mind as a favourite right now, given that set of circumstances and how beautiful it is. Although Infinite Being is close behind 'cause it's wonderful.
If it's any final boss overall though... probably Yuyuko's or Kaguya's fight as accompanied by the music due to epic buildup and last spell; or, for a single track, Fate of Sixty Years