I am also confused about the fact that your three acceptances are in very different fields.
What do you want to study? What do you want to do with your career over the next few decades?
Assuming that your PhD is fully funded, …
To me this is what matters. You are deciding what career you are going to take on. You are deciding which lab and what advisor or small group of advisors you are going to be working with for the next five or six years. This is what matters.
I do not think that the overall reputation of the three universities matters when you are deciding which PhD to take on. You are not going to attend the university as a whole. You are going to be working with a very specific and very specialized small part of the university.
Down the road, hiring managers (or faculty if going into academia) will know about the reputation of your advisor and your specific lab in your specific field.
I do not know if you can be 100% certain before you start your program. However, this specific issue was a big part of how my daughter chose the PhD program that she is about to start later this year.
If your PhD program is not fully funded, then this brings up an entirely different set of issues.