Hi,
Yes, if you're sure the stall current is below what your meter can handle, otherwise use an external shunt of known resistance and measure the voltage drop over that - method doesn't really matter, as long as you get the numbers without harming the motor.
If this is for a protection circuit, to cut the power at stall, perhaps make it so that it cuts way before stalling, since a "semi-stalled" motor might still be ruined - that's why some motors have temp. sensors installed.