Metroid Prime 2: Echoes in the lead.
GameRankings.com ranks games according to the reviews in major online publications. This is recent chart for top 10 GameCube games 2004 (updated December 26):
Top 10 GameCube games 2004
1. Metroid Prime 2: Echoes Nintendo 92.4%
2. Pikmin 2 Nintendo 90.0%
3. Madden NFL 2005 EA Sports 89.6%
4. NCAA Football 2005 EA Sports 88.1%
5. Paper Mario: The Thousand-Year Door Nintendo 88.1%
6. Tiger Woods PGA Tour 2005 EA Sports 88.0%
7. NASCAR 2005: Chase for the Cup EA Games 87.7%
8. MVP Baseball 2004 EA Sports 87.3%
9. Metal Gear Solid: The Twin Snakes Konami 87.1%
10. Viewtiful Joe 2 Capcom 86.7%
