if lys and tyrosh became incredibly rich and prosperous despite being tiny islands, why cant the steptones similirly become prosperous?

They could potentially, but they lack a lot of the advantages that Lys and Tyrosh had – Lys and Tyrosh were set up as colonies by a rich metropole, so that means an outside power was putting in physical and human capital to set them up; they have what should be a rich hinterland; and of course, they have a first-mover advantage when it comes to trade. 

So the Stepstones would be starting from scratch with little physical or human capital, they don’t have an agricultural hinterland to feed a growing population unless they want to jump into the fight for the Disputed Lands, and they’d face very stiff competition from Tyr and Lys and Myr, who aren’t about to let a bunch of pirates into the market.