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Raphael was the canon leader in the movie.
Yes, you are right, in every other TMNT product, Leonardo is the leader.
But don't blame the song, blame the creators of the movie. This song is epic (way better the utter garbage that was Ninja Rap).
Side note: when I was in college, I went to a local band's concert (Estradasphere), where they did T-U-R-T-L-E Power live. My life peaked that day.
Hourglass Plot: The movie starts with Leo, Don, and Mike being carefree and joking around while Raph is the moody, angsty teen who prefers being alone. He also ends up butting heads with Leo over his leadership skills after Splinter is abducted and questions why they don't go look for their sensei right away, while Leo tells him they should be patient and wait for April to get more information to help them out. After he is beaten to near death, Raph's attitude towards Leo changes a lot after seeing the latter's Big Brother Instinct towards him.
However, Raph goes too far by accusing Leo of acting like he's their "great leader" when it's quite clear that Leo's just trying to keep it together under a scary situation, but then Leo makes it by telling off Raph for acting like a jerk and that his attitude won't help their situation, which makes Raph storm out of the room, leading him to get ambushed and nearly killed by the Foot, all because he was fueled by emotions alone.
At best, they had a leadership struggle, which Raph didn't win - Leo was the leader both before and after their disagreement.