You can find Ioun stones by searching for "ioun". Some are combined within a pseudo-item entry with individual stones hidden from the list, others (the ones from Kwalish) are shown both separately and within the combined entry:
https://www.dndbeyond.com/magic-items?filter-type=0&filter-search=ioun

If you are not specifically looking for Ioun stones, and just want any item with a bonus, you might try filtering for that instead. The pseudo-item has been tagged with some of the available bonuses: "Bonus: Armor Class, Bonus: Charisma Score, Bonus: Constitution Score, Bonus: Hit Points, Bonus: Intelligence Score, Bonus: Strength Score, Bonus: Wisdom Score, Bonus: Dexterity Score". This ensures that it is found when filtering for one of those:
https://www.dndbeyond.com/magic-items?filter-type=0&filter-effect-type=1&filter-effect-subtype=5
https://www.dndbeyond.com/magic-items/ioun-stone

The tag for "Bonus: Proficiency Bonus" is missing on the pseudo-item entry. Filtering for this bonus finds neither the specific "Ioun Stone of Mastery", nor the combined pseudo-item entry:
https://www.dndbeyond.com/magic-items?filter-type=0&filter-effect-type=1&filter-effect-subtype=814
https://www.dndbeyond.com/magic-items/ioun-stone-of-mastery

Please either add this tag on the combined item, or set the Mastery stone to show up separately in the list like the Kwalish stones.