Which scientific discovery was most ahead of its time?

Cases where scientific knowledge was in fact lost and then rediscovered provide especially strong evidence about the discovery counterfactauls, e.g. Hero's eolipile and al-Kindi's development of relative frequency analysis for decoding messages. Probably we underestimate how common such cases are, because the knowledge of the lost discovery is itself lost — e.g. we might easily have simply not rediscovered the Antikythera mechanism.

General relativity is an obvious candidate. While special relativity was hanging in the air, and so was quantum mechanics, there was no urgency to improve on the Newtonian gravity at the time. There were a few small discrepancies, like the perihelion of Mercury, but not until the discovery of expanding universe a decade later it was obvious that a new theory was needed.

Possibly Antonie van Leeuwenhoek's study of microorganisms; he made microscopes that were much better than anyone else's at the time, and he kept his methods secret and they weren't properly reverse engineered until the 1950s. (Conventional lens making techniques did catch up, and people like Robert Hooke had been investigating biology on micro scales, but he was probably a generation or so ahead of everyone else.)

Scientific progress is not at all continuous and not systematically forward. There have been many periods of scientific regress. The most famous is the Dark Ages between Antiquity and Modernity, hence Luke's example of Hero.

But regress is all over the place, even in well-known examples of progress, like the Italian Renaissance. People often say that Renaissance art began with Giotto or maybe even so specifically with his invention of perspective. But, actually, most accounts of Renaissance art skip ahead a century from Giotto's death in 1337. In particular, perspective regressed and was reinvented in 1413 by Brunelleschi. And this wasn't even an independent discovery: Brunelleschi could see Giotto's work and knew that better was possible. *

Going back to Hero, "ancient Greece" is a bad category. Hero isn't the pinnacle of ancient Greek science, but a figure of a Roman era of rebirth after a dark age 150 BC – 50 AD during which we know the names of no scientists. In fact, almost everything Hero writes about he attributes to Ctesibius (d. 222 BC). If he is truthful about his sources, then there was a either a 250 year pause in pneumatics or there was more progress that was lost in the interim. In general, a controversial question is whether the rebirth in Roman Alexandria reconstructed and surpassed Hellenistic Alexandria or whether it was only able to understand a few books.

* Lorenzetti (d. 1348) seems to have been pretty good at single buildings, but bad at putting them together. Compare the only city I can find by Giotto.

There are plenty of accidental discoveries that we might imagine happening much later - but I don't feel like this should be enough, because it's not that they were surprisingly early, they were just drawn out of a very broad probability distribution.

I'm more satisfied with disoveries that not only could have happened later, but happened when they did for sensible local reasons. Example: Onnes' discovery of superconductivity. Not just because superconductivity was discovered very rapidly (3 years) after the necessary liquefaction of helium, when it conceivably could have taken a lot longer to properly measure the resistance of mercury or lead at low temperatures. But because Onnes' lab in Leiden was the first place to ever make liquid helium to cool superconductors with, and it took 15 years for anyone else in the world (in this case, Toronto) to start liquefying helium!

In short, to my mind being ahead of your time is the opposite of multiple discovery - we push back the luck one step by asking not for a lucky break, but for a sensible and straightforward discovery that could only have happened in a very unusual place.