[seg9585]

Two different gearboxes will never produce the same exact output power/torque/rpm, because small variances in gear friction and efficiency can drastically change the performance.
I assume you don't have encoders you can use to match the wheel speeds?
If not, then simply add a "bias" multiplier to the motors in the faster gearbox so its max speed is slower such that it matches the other gearbox.

For example, if the robot is steering to the left, that means the right gearbox needs to be slowed down:

bias=0.9; // Figure out what number to use here until the robot drives straight, should be between 0 and 1 noninclusive

leftmotor.set(joystick.getY());
rightmotor.set(joystick.getY()*bias);