Wow ancient thread.
I don't know if the question was meant to be which current lineup is better, or which band has the better discography. I'm going to assume it's the latter. So it's got to be Helloween. Walls of Jericho, the Keepers albums, and then they added to those with albums like Time of the Oath, Better than Raw, Gambling with the Devil and the Dark Ride.
Gamma Ray has amazing albums like Land of the Free, Power Plant and Majestic, but they're not standing on the shoulder of giants, so they don't get the benefit of adding Walls of Jericho and Keepers to their discography.
As for which band is better right now... damn, that's a tough one. Both bands rule!