I get his alchemy up to 15 as soon as possible, then build it with potion-mixing. If I have a bishop or alchemist ... the ninja does all the mixing.I build throwing (shuriken, knives or sling) and let him carry acid bombs and cherry bombs. Build critical kill to improve the effectiveness of his throwing.
I get the following spells as soon as possible: Toxic cloud, blinding flash, heal wounds, acid bomb. Monsters are frequently out of throwing range in the first round so he is free to cast disabling spells. Spells like whipping rocks are more limited in range but also useful.
He is the team lock-picker if I don't have a rogue.