Well, this is a long list of calculations, so if I've got something wrong, someone please point it out.
Formula for Gyro Ball:
>Base Power = 25 × (Target's Current Speed / User's Current Speed)
But no greater than 150 base power.
While the Base Power is dependant on relative speed, you also need to factor in attack stat, since Gyro Ball is a physical move.
Magnemite's highest attack stat at 100: 185
- lowest speed at level 100: 85
Magnezone highest attack stat at 100: 262
- lowest speed at level 100: 112
Base Power = 25 × (372 / 85) = 25 x 5 (rounded up) = 125
Base Power = 25 × (372 / 112) = 25 x 4 (rounded up) = 100
Magnemite's base power for Gyro Ball would be higher.
According to Pokemaster, this is the formula for calculating attack:
> USER_ATTACK = (2×USER_LEVEL + 10) × USER_ATTACK_STAT × BASE_POWER
Manemite attack = (2x100 +10) x 185 x 125 = 5.087.500
Magnezone attack = (2×100 + 10) × 262 × 100 = 5.764.000
So actually, Magnezone would deal more damage, due to its higher attack stat.
Of course, Gyro Ball also depends on your opponent's speed, what your Pokemon is holding, its EVs/ IVs, your opponent's EVs/ IVs, and what your Pokemon's ability is as well (e.g. Analytic). We can discount STAB in this case, since both Pokemon will receive STAB from Gyro Ball.
I really hate numbers.