Black pearls are a rare harvest from Black Lotus. You can find Black Lotus flowers in Mooshu, and then off and on in various higher worlds like Celestia, Zafaria, etc.
There are transmute recipes available from the crafting shop in Grizzleheim (main area of Northgard, off to the left side once you go through the gate), and from a vendor at the back left side of Celestia's main camp. If you're just starting Mooshu, then you should buy your transmute recipe from the guy in Grizzleheim, as you won't be able to reach Celestia for quite a while yet.
In Mooshu, Black Lotus flowers tend to grow at the ends of the streets, often near the little dojo houses, hiding behind rocks, etc.
And last ... if you go back to Krokotopia and fight the little blue manders in the Krokosphinx a few times, they'll drop Pink Dandelion seeds. Keep those! Go home and plant them! The pink dandelions drop all kinds of rare reagents needed for the crafting quests.
Pink dandelions are your friends. They also drop blood moss and a bunch of other nice reagents. Blood moss is expensive in the bazaar and snapped up super quick. But it is in a lot of crafting recipes.
Biti Nirini is your man. Or Krok. Or krok man? Lol. Seriously the most effective way to get pinks. After half an hour of splashing him with tempest I had five pinks.
Only transmute if you are desperate but even then it gets really painful.
I know this post is over a month old now but just wanted to add in my two cents.