The money was for buying Arturro Marquez
A gang of Hungarians had arranged to purchase Arturro Marquez (Castulo Guerra), a man who could identify and incriminate Keyser Söze.
Agent Kujan (Chazz Palminteri) spells this out in a scene very near the end of the film:
@ 1h32m33s, between Agent Kujan & Verbal Kint (Kevin Spacey)
Kujan: Arturro Marquez -- ever hear of him?
Verbal: What? No.
K: He was a stool-pigeon for the Justice Department. He swore out a statement to federal marshals saying that had seen and could positively identify one Keyser Söze. It says right here in the report. He had intimate knowledge of his businesses, including, but not exclusive, to drug trafficking and murder.
V: I never heard of him.
K: His own people were selling him to a gang of Hungarians, most likely the same Hungarians that Söze all-but-wiped-out back in Turkey. The money wasn't there for dope. The Hungarians were going to buy the one guy that could incriminate Keyser Söze.
Let's ignore the final bit about which Hungarians are buying Marquez, because it really doesn't matter, and is clearly Kujan's own off-the-cuff supposition based on Kint's questionable Söze origin story.
The rest of Kujan's theory is reliable.
The most obvious reason is that this information was independently acquired by federal marshals. Marquez almost certainly told the truth, because his own lawyer, not to mention the Justice Department, would have told him that he would probably be required to identify Söze and testify against him in court, and if he refused or failed to do so, he would lose whatever deal he had negotiated with them, as well as facing additional criminal charges for lying while under oath (hence the phrase "swore out a statement").
Another reason to believe this story is that we see that Marquez really was on the boat, and was killed. This takes some effort to prove.
There's a brief scene where a scared man is hiding in a locked room on the boat, and he starts freaking out when a guard checks on him:
@ 1h24m31s, between Arturro Marquez & an unidentified guard
Arturro: He's here. I know he's here. That's him! I'm telling you, that's him! I know he's here! You've got to understand, that's him!
Guard: Shut up!
A: That's him, do you hear me! I'M TELLING YOU IT'S KEYSER SÖZE!!
The man is wearing something that looks like a tan smoking jacket or vest sporting a busy pattern shaped like a peacock feather.
We see a corpse floating in the harbor wearing the same distinctive jacket much earlier, at 17m57s.
You might wonder how we can be sure the scene with the guard really happened. After all, Kint is an unreliable narrator, and the movie seems willing to show us convincing portrayals of some of his other lies, so why not this, too?
Consider this: Verbal Kint cannot tell Agent Kujan about the freak-out scene because, as shown in that scene, he was not present (which is also his story: he wasn't there). Maybe the truth is that he really was there, spying on them through a vent or something, and now he obviously wants to lie to Kujan about that detail. Well, he will not accomplish that by saying, "elsewhere on the boat, in a room I was nowhere near, a guard had a private conversation with someone who wasn't me, and then closed the door." If that really were what occurred, how would Kint know it?
So, when the movie shows us this scene, it cannot be because Kint tells Kujan about the event. The only reasonable conclusion is that this event really did happen, exactly as we see it.
Finally, we know the man in the smoking jacket is Marquez because Agent Baer tells Kujan & Captain Rabin (Dan Hedaya), shortly before we see Marquez's execution:
@ 1h22m41s, between Baer, Kujan, and Rabin
Baer: Boy came across a body on the beach this morning, thrown clear of the boat, burned, shot twice in the head. Two guys from the Bureau just identified him.
Kujan: What else?
Rabin: His name was Arturro Marquez, a petty smuggler from Argentina.
Also, when Kujan mentions Marquez later, the movie cuts briefly to him, dead, in that room & jacket.
Thus: the money was there to buy a witness who could identify and incriminate Keyser Söze, and who had in fact promised the Justice Department he would do so.
Sidebar: it has been said here and elsewhere that we can't trust any of what we see in the movie because everything Kint says is probably a lie.
That is taking things too far. Yes, Kint is a liar, and potentially everything he says is false. However, as mentioned in this post, Kint cannot be lying about any scene in which he is not present, because it is very obviously impossible for a person to report what happened at a time and place they were not present. So, if the camera shows you something where Kint is present, it may be a lie, but if Kint is not there, it probably has to be true.
It is also worth noting that the most convincing lies have a kernel of truth. So, if this were a real situation, it would make good sense for him to tell a story that is mostly true, changing only the details of his involvement, and also of course the names.