This doesn’t have to be a problem. This is the game they seemed to want, and you seemed to be OK giving it to them: now you just need to understand what the ramifications of this kind of game are. Their wealth pushes them past a lot of mundane problems—like travel—so challenge them with greater, more supernatural threats. Magic is fantastically expensive, after all.
Because if you have been giving out levels like candy, then yes, they are supposed to be able to buy a boat on a moment’s notice with some spare change. That’s part of what it means to be high-level (or really, even mid-level) adventurers.
The expected wealth of a 5th-level character is 9,000 gp (or 10,500 gp, in Pathfinder), each. A 10,000-gp boat is quite an investment for a party of four 5th-level characters. The expected wealth of a 10th-level character is 49,000 gp (62,000 gp, Pathfinder): for a party of four, with somewhere around 200,000 gp between them, that’s not much. By 15th-level, they instead have 200,000 gp (240,000 gp, PF) each, so four of them have nearly a million gold pieces’ worth of funds. A 10,000-gp boat is not a serious expenditure.
You know those scenes in TV shows and movies where someone walks in and just buys things no one thought was even for sale, by just casually writing a check for fantastic sums of money? Bruce Wayne just buying the hotel so his lady friends could play in the fountain, Mr. Saito purchasing an entire airline rather than trying to bribe all the appropriate personnel because “it seemed neater.” Those things: D&D 3.5 and Pathfinder characters can be those characters by mid levels.
More importantly, powerful options for transportation, such as teleport, greater teleport, and plane shift become available at high levels. A 10,000-gp boat might be cheap, but a high-level character wouldn’t buy one anyway: they can move much, much faster than merely sailing anyway.
And that’s normal. If you have been offering more wealth than this, then you are going beyond recommended values, so the cost of a boat becomes trivial sooner than this. But it’s really not anything new, just early. By giving more wealth than normal, you are suggesting that something like a boat is not supposed to be a significant cost to the party. And that’s OK.
The reason that this happens is because wealth is directly tied into character power. In order for characters to keep up in power, in addition to levels and class features and so on, they also need magic items. And magic items are, compared to any and all mundane expenses, fantastically expensive. An entire boat costs 10,000 gp: a +2 adamantine dagger costs more than that. A +5 longsword costs much, much more than that. Basic ability-enhancement items (gloves of dexterity and so on) cost 60% more than a boat in the +4 version, and in the +6 version, cost three-and-a-half times what a boat does. A single mid-level magic item is worth enough to hire a score of fantastically-skilled laborers to work non-stop on something for most of a year.
Such are the rewards of adventuring. Considering their life expectancy, plus the need to invest so much of their money in preposterously expensive magic items just to have any hope of survival, maybe that’s not so ridiculous.
But ultimately, you don’t really need to have a problem here. Mundane concerns are now beneath them in all but the most ludicrous amounts and qualities. They can have the fastest, most luxurious mundane boat in existence, they can even afford to pay premiums to get it now and so on. That’s because they are adventurers, with serious, magical problems to thwart, and magic problems require magic gear and magic gear costs several fortunes.