All you need are wordlwide emision regulations. Better qulaity fuel or eniges better tued to emisions might make a lot of difference. There currently is economic benefit to tune a ship for better emissions. Even putting it in a harbour for 2 weeks to tune the engine (don't know if technical possible) will set the owner back a lot of money. He will not do it just for emision.
You will not need large innovations. Clean emisions is already understood, and used in power plants. YOu just need motivations.
by the way, Carbon (CO2) exhaust: some idusties, heating, and electircy generation might win more.