Pucci was one of the better villains in JoJo, but would I say the best? ....Not quite.
He indeed had some stand out qualities. His fleshing out through his backstory was excellent, he had enough quirks on his own to stand out as an individual such as his OCD regarding prime numbers and the premise of having a minion of DIO carry on his legacy, not to mention the differences in their personalities help elevate Pucci when it comes to being DIO's successor. It also helps that compared to a lot of the other villains that didn't get actively involved for a long time due to arrogance or another reason such as DIO and Diavolo, it was a breath of fresh air to see Pucci actively being present throughout the majority of Part 6 to achieve his goal, not to mention being far more efficient in his actions than them. With that said, it makes sense how he came closer to achieving his goals than any other JoJo villain.
However, he's far from Araki's masterpiece of a villain. Leaving aside the question of where was Pucci in Stardust Crusaders as there's a few minor explanations for that, Whitesnake's use in general is pretty damaging for the writing as most of the fights involving it made it seem as though it was asspulling new, overly specific abilities for the sake of extending the plot. Alongside that, Pucci's actions being solely for DIO's legacy limit his sense of agency when having no personal desires of his own. It does make him be more distinguishable as a villain, but also causes his goals to be overly narrow when just amounting to "muh heaven."
As for the hypocrisy of his actions in the name of God, that's a mixed bag on its own. Other characters at least point out the contradiction in his action to make it an intended character trait, though it still comes off as a bit unfeasible how blinded he could be to using religion as a shield when he had already gone ahead to essentially deify DIO and, thus, make his actions completely heretical. By comparison, Funny Valentine was a far better case of a JoJo villain using a concept beyond themselves to justify their actions as they remained consistent with both the political beliefs of nationalism and Valentine was consistent with them (to the extent even Johnny conceded he did nothing wrong was more justified than himself).
A great villain in concept and one of the most unique in anime/manga, though still victim of some heavy writing problems when it came to writing a contradictory character.
7.5/10. Would rank him as 3rd best JoJo villain just underneath Kira and a few steps below GOAT Valentine.