The CraftLootTable type does not have any implementation for setting LootContextParameters.TOOL. I was able to fix this in my own plugin by making an alternate type and adding the following line:

setMaybe(builder, LootContextParameters.KILLER_ENTITY, nmsKiller);
// If there is a player killer, damage source should reflect that in case loot tables use that information

//NEW LINE
setMaybe(builder, LootContextParameters.TOOL, (CraftItemStack.asNMSCopy(context.getKiller().getItemInUse())));

setMaybe(builder, LootContextParameters.DAMAGE_SOURCE, DamageSource.playerAttack(nmsKiller)); 

I imagine theres a better way of fixing it, I'm very new to this.

Anyways, this parameter is necessary when generating loot tables with fishing contexts which as far as I can tell does not work in current spigot implementation.