There have been four different users that have been #1 on Pokebase. I got these using the Wayback Machine, so it is impossible to pinpoint the exact dates that each user took the lead. This means there may be slight inaccuracies — e.g. a user may have gotten #1 before it was first recorded by the Wayback Machine. That said, the general time frames are below.
Pokemaster: April 2010 - October 2010
Though the first snapshot of the users page is in May 2010, it's easy to assume that the creator of the site had to have been #1 at its inception a month earlier.
DarkTyphlosion: October 2010 - January 2014
As an early member, DT took a commanding lead and held it for years. There is a significant gap between snapshots in the last months of his lead, so he may have held the position for slightly less time than what's shown.
Mewderator: January 2014 - July 2025
It is difficult to say whether Mew and DT swapped positions back and forth at any point in 2014, but this is the first instance of Mew appearing at the #1 spot. This is a rank he would hold for over 11 years — the longest of anyone. Mew reached #1 on January 2, 2014, per the congratulatory post the next day.
Amethyst: July 2025 - present
Rising on July 16, 2025, Amethyst is the most recent user to hit #1 and also the only one we have a guaranteed ascension date for. As an unbiased observer, I am sure his reign will be long and prosperous.