the card reads "players must randomly choose a crystal..."
random - by color or quantity? (for example, if I have 3 red & 1 blue crystal, is the chance that I lose my blue 1-in-2 or 1-in-4?)
It depends on how you decide to choose the color of the crystal to be lost. If, as others have already said, you throw your four crystals into a cup, then the probability that you will lose the blue one is 1 out of 4.
If you roll the mana die to decide it will be 1 out of 2. This assumes each player rolls a die and keeps rolling until the color on the rolled die matches one of the crystals in their possession.
Personally, I think the first method is the best one as you are literally choosing from the actual crystals.