The way I think about it, the greatest achievement of chemistry in the last fifty years or so is not any particular discovery but a validated philosophy; that given the time, funds and motivation, we can make virtually any molecule or material by the application of rational physicochemical principles. Of course we are still far from designing functionality on demand (it's much easier to make structures), and pure rationality in designing molecules is still a fond hope since most rational design of molecules like drugs is what I call "rational in retrospect". But what we have is still a substantial achievement.
We can make this question even more general. What is the greatest (or perhaps the top three greatest) achievement of chemistry since it emerged from the darkness of alchemy? Comments are welcome and there are many choices. Lavoisier's enumeration of the differences between elements and compounds, Dalton's atomic theory, Wohler's synthesis of urea, Mendelev's periodic table, Gibbs's application of thermodynamics to chemistry, Staudinger's unveiling of the nature of polymers and Pauling's application of quantum mechanics are all worthy candidates. But I would venture that none of these single achievements was as important as the development of a general philosophy of chemistry; that by the application of principles grounded in other disciplines like physics combined with carefully tabulated empirical knowledge about the properties of substances, one can crack open the mysteries of the structure of matter and use this hard-earned knowledge to synthesize new materials never seen before. It was the coming of age of the precise yet usefully capricious mix of rigor and empiricism that defined and continues to define modern chemistry.
Indeed, one can broaden the question to include other disciplines and even all of science. What single achievement was the greatest in all of physics? I would say it was the discovery that relationships between properties of objects can be precisely quantified by proportionality. Biology? The meticulous, exhaustive classification of species and creatures combined with the knowledge of the workings of those creatures at the molecular level.
And so it goes for science itself. What was the greatest discovery in all of science? Some may say it was Newton's laws of motion, or Einstein's theory of relativity, or quantum theory, or Darwin's evolution by natural selection, or Maxwell's laws or those of thermodynamics. But while these discoveries are undoubtedly paramount, they miss what is the most important contribution of science to the world. This contribution was the well-defined process of hypothesis testing and experimentation and formulation of theories that allows us to divine new truths from nature. The process is messier than it looks on paper but it has still served as a most rewarding guide. It has allowed science to make the modern world in its image.
The greatest discovery is not an island but a whole continent of ideas.