A 2S LiPo would be better as it has a nominal voltage of 7.4 V. Increasing the voltage applied to the gearmotors increases the performance of the gearmotor (including the speed), but as I mentioned previously, it also puts more stress on the gearmotor. The speed of the motor depends on the load you have on your gearmotor, but at 6 V, you should be fine if you run the gearmotor at 30% of the stall current. You can find additional information in the performance graphs on the datasheet for the micro metal gearmotors.
The mAh rating on the battery rating is about capacity, and does not have a significant affect on the speed of the gearmotors. If want to know more about battery ratings, you might find this blog post about battery capacity helpful. You should select the battery based on the how much battery capacity you need.
You can also use a voltage regulator to step down the voltage from a 3s LiPo to a more appropriate voltage, but you should make sure the regulator can handle the stall current of both gearmotors (2 A each at 7.5 V). From a quick look, it seems like the regulator you mentioned is a constant voltage regulator, not constant current, so the amount of current it will be able to handle will be based on the input voltage and other factors like heat.
Grant