Hard for me to pick one singular favorite. I love the music for Kraid's Lair in Metroid, Red Brinstar from Super Metroid, both tracks from Sector 4 (AQA) in Fusion, Underwater Frigate Reactor Core from Metroid Prime, Quadraxis from Prime 2, Bryyo from Prime 3, and basically everything from AM2R.
If I had to pick which (official) game in the series has the best music though, I'd probably go with Prime 2. Pretty much every area has great music (maybe except Agon), every (non guardian) boss has a great track, and the entire OST has thematic structure that matches the atmosphere of the game.