Unusual_
He got the money from Vacher/Marcel.Vacher was the Heisenberg of Fontaine and was the biggest drug lord in the nation.Since he’s dead,and Issac knows where his base of operations is,all his wealth,notes,and connections where up for grabs.Which brings in the possibility of Issac taking over the drug trade of Fontaine,since he has Vacher’s notes on how to make it.If not,then there is going to be a huge power grab that going to happen in the underworld of Fontaine and Navia is going to be in the middle of it,as well as trying to look for the now missing Marcel.Navia’s story is now going to be way different then canon now that Marcel went out of the picture the way he did.That and the effects of the primordial water won’t be reveal to all of Fontaine until much later or in a different way since it can’t happen the same way anymore(most likely time will be when the primordial sea hits Poisson).
Isaac can also have laundered whatever money he needs using his cafe,or whatever Marcel has,if he knows how to do that without getting caught that it.He is at the nation of Justice after all and they are not stupid,they have good,if not as good,or even better in some ways of investigation that can trip him up or get him caught if he is not carful.The system has been covering him so far and will probably continue to do,but he still should be careful as the system can’t cover everything.