Which are the best universities in Europe to pursue a Master's degree in Mechanical Engineering with specialization in Fluid and Thermal Sciences?

First I appreciate for your interest in pursuing Masters in CFD and the place you have chosen. I have a very basic question, what is your area of Interest. Are you interested in learning about the application of the CFD Principles or the basic architecture. For example, I have seen people visit Europe for gaining Masters in CFD and their motive is entirely different, they aim to get Master in ANSYS and the like. If that is your aim, I am sorry, this is not the right place. Most Universities in Europe teach you whats behind these ANSYS Software, how do they work, how the NS Equations is solved and the likes. There are also other methods for solving the problems without considering the NS equations like the smooth Particle flow, Rigid Body assumption etc. To be frank 75 percent of the class hours you will be fighting with the mathematical equations. Remaining 25 percent how to program these equations. Finally you will be able to bring your own code for solving such equations and verify your result with Ansys Output. If this is your research interest, I can suggest you to choose Europe. Else, Please reconsider your interest with Masters.

The best universities for Fluids and thermal sciences that I know of in europe are ETHZ, Tu9, Tudelft and maybe some french aerospace universities.

https://www.vki.ac.be/

I have already answered something like that here: Unfortunately, my experience about the academia in Europe is limited by the word of mouth and impressions created by the literature that comes out. I do not want to misguide you by giving you an incomplete (or perhaps incorrect) answer, people who have themselves studied/researched in Europe may be better suited to answer this question properly.