There has been a lot of speculation about what this could be. Some combined this discovery with the fact that some Weapon Manufacturers are missing from the game and a new weapon rarity tier would be possible.
However, the official Tiny Tina’s Wonderlands channels informed us that there is no such thing as a rainbow weapon rarity in the game.
Personally, I thought that these crystals were a rare currency like Eridium or Seraph Crystals. However, we now know that these rainbow crystals are part of Tiny Tina’s Wonderlands End Game. You can get these crystals in the Chaos Chamber.
You can use the rainbow crystals to purchase specific loot types in the Chaos Chamber. These crystals don’t carry over from run to run. So use them or lose them.