Going with the assumption that mystery (whodunnit) ≠ suspense, and judging them solely by the mystery element: Hyouka for me. It’s a grounded anime with nothing crazy going on, so the focus is purely on the mysteries. (There are the usual slice-of-life, school-life stuff, but those are secondary / don’t distract from the mysteries.)

Some runner-ups:

• Oddtaxi - It has one of the strongest twist I have seen in anime.
• The Apothecary Diaries - I enjoyed the political elements in addition to the mysteries.
• Gnosia - I enjoyed playing along as though I am one of the participants.