I didn't find any references to costs of higher education, so I'm going to do a real world comparison.
As it's well said in @NautArch's answer, this is not an accurate comparison, and I fully agree that a fantasy world is going to have a lot of nuances that will vary the prices of products, like guild based economy where competition doesn't exist and holds prices, for instance. But I still think it can serve as a reference to how much things cost in a more broader sense. The more you compare what things cost between them the more sense you can have of how much money (meaning coin) itself is worth.
It's impossible to find the real price of a product or service that exists only in fiction. There is no real way to compare it with something real moreso when the used coin itself is not real. This is not me saying "This is the accurate price". It's just "If X costs Y in our world, and Z in fantasy, you can compare it and have a clue of how much something is worth". Maybe the result is outrageous, maybe it makes sense to you. In the end it's fiction, so take this only as a way, or a tool to decide on the cost, nothing else. In the end prices are subjective. Economy is very complex, and in a roleplaying game, every product and every coin is put in circulation by the authority of the DM.
A little bit of math
A spiced apple cinnamon wine bottle, which is likely a cider, costs 5 silvers in Eberron. (Got the reference from here)
In Madrid a bottle of cider costs around 3€.
In Madrid higher education costs an average of 1,609€ a year.
Then we do a rule of three.
0.5 [gp cost of cider in Eberron] * 1,609 [Higher education in Madrid] / 3 [Cost of cider in Madrid] = The average cost of higher education in Eberron should go around 268.16 GP per year. This is more or less the cost of a coach with a horse, so it's pretty expensive.
Take in mind this is a rough approximate for an average university cost. Values could vary depending on market conditions. But I think it's a good measure of the basic cost, you could go up from there.
Probably magic schools in Eberron take a lot less students, which means increased prices, so you could get a more accurate price if you could know how many students does a magic school in Eberron have vs how many students does the average college or university have.
Since we got the cost of studying in Harvard from the answer user @Phillip gave us before (67,580$) we can use this method to do a similar comparison with the cider bottle in USA (around 5$ for a litre) giving us a total of 6,758gp a year.
DM controls the economy
But definitely, this is just another perspective and more of a thought experiment. @NautArch's answer is the most practical in regards to the game. The DM decides the value of money and controls all the economy, so the DM should decide.