Last year we used I2C to successfully control an Arduino.
You can see the Java command here:
https://github.com/Team3574/RKellyBo...ems/Bling.java
And the Arduino code here:
https://github.com/Team3574/RKellyBo...hoot/shoot.ino
Note the address used by the cRio is 2 * the address used on the arduino.
If you choose i2c, you will also need to use the ribbon cable to connect the cRio to the digital breakout.