Which preposition to form the superlative in a place

I think both are ok. just like using ” ‘s” and “in” in english.

For your second sentence, It would be between “de” and “en”. “de la” is good too.

I prefer de which is more idiomatic in both cases:

C’est le bâtiment le plus haut de Paris.

Le plus haut de Paris is a single unit while le plus haut à Paris is less coupled. You might say:

À Paris, c’est le bâtiment le plus haut.

while:

De Paris, c’est le bâtiment le plus haut.

would be much less natural and possibly ambiguous.

Same for the second sentence:

Penses-tu que Paris soit la meilleure ville de France ?

It still sounds a little odd though as something is missing for it to be complete and idiomatic, like:

Est-ce que tu penses que Paris est la meilleure ville de France pour s’amuser / trouver du travail / se déplacer en transport en commun / etc.

C’est le bâtiment le plus haut ___ Paris

You have to use “de”.

Superlative: You have the form: le plus + adjective + de
Grammatical variants: le/la/les plus…. de/du

Ex:

If you write:

C’est le bâtiment le plus haut, à Paris

Sounds incorrect and weird. Like jlliagre said:

À Paris, c’est le bâtiment le plus haut.

could be said, but the real superlative form is much better.