The EN to the regulator should work as well, but since that will shut off power to the GPS you should make sure to set any IO pins that are outputs to the GPS to tri-state (ie inputs), or drive them low while you have the power off.

For the UART TX output that means disabling the uart to get control of the IO pins.

Also, you may need to pull EN low for longer than 1ms. When the regulator shuts off it'll probably take a while for the GPS 3.3V to drop.