Well, it depends on how you judge the games. Metroid Prime and Resident Evil 4 are my two favorite games from either console's libraries. However my favorite Wii game is Twilight Princess simply because to me that is a Wii game every bit as much as a Gamecube game as they launched simultaneously, and I consider MP and RE4 Gamecube games that came out later on Wii.
So if you're just comparing all the games from both consoles to someone who has never played them before, then yeah I could see the Wii coming out on top. It has Twilight Princess, Metroid Prime Trilogy, RE4, and better games of Smash Bros, Mario Kart, and a far better Mario with Galaxy. Not to mention access to the entire VC library.
However to me, Prime and RE4 on the Cube are legendary; more-so than any Wii game so far. I just don't hold the ported remakes of the Wii versions in as high regard. I'd consider the best Wii games to be Twilight Princess, Galaxy, SSBB, Prime 3, MK Wii, Zack and Wiki, etc. So looking at it that way I think that, SO FAR, the Gamecube still probably has the better of the great games, for its time anyway:
Metroid Prime, RE4, Wind Waker, Eternal Darkness, Resident Evil remake (Far, far better than the PS1 original), Viewtiful Joe, F Zero GX, Rogue Leader, etc.