I took it to mean that Pegsworthy heard from Harrigan that Harrigan himself stole the ship, and was probably in a nearby port getting supplies and selling the Man's Promise's loot and raising his own infamy by boasting about it. Pegsworthy could have overheard it in a tavern, left the city the next day, came upon the Strix the following day, then Rickety's a few days later.
As for Harrigan finding out about the PCs, Caulky can tell him if she gets away in book three. He could also just naturally hear tales of the PC's actions as their infamy grows, realize Plugg never reached Port Peril, and that he used to have some crew matching the names of these new upstarts.
