What voltage does the RPi put out, and what voltage does your Arduino take? If they match, or the Pi is a bit less than the Arduino, it's simply pin to pin (and connect grounds).
Directly from the Pi output to the Arduino input. Not from between the resistor and led. You will need a common ground connection also.
Assuming your Arduino is 5V, then any voltage around 3.0V or above should read as HIGH, so the 3.3V from the Pi should give a HIGH reading.
However, if your series resistor is too low, drawing too much current from the GPIO pin (16mA or more) then this could drag down the output voltage so much that it is no longer above 3.0V, causing the Arduino to read LOW even though the led is on.