If you put your transfer case to neutral...you should be fine...putting the transfer case to neutral effectively 'disconnects the transmission from the axles.
However, you still might be accumulating miles on your 4runner if the wheels are rolling.
Not sure on the 4runner, but on a XJ cherokee, the speed sensor/gear is on the transfer case instead of the transmission.
But if you have an electronic speedo (no cable)...I wonder if it will still register mileage with the vehicle turned off???