Most rankings I see always put his early Alex Cross novels at the top, and for good reason. 'Along Came a Spider' and 'Kiss the Girls' created the blueprint. The pacing is relentless, the villains feel genuinely monstrous, and Cross himself has a vulnerability that later protagonists sometimes lack. Everything after, even the solid ones, feels like a variation on that original, perfectly tuned formula.
That said, I find the constant churn with co-authors makes the 'best' list really uneven. A title like 'The President Is Missing' with Bill Clinton gets attention, but it reads more like a political procedural to me. For pure, classic Patterson thriller mechanics, you can't go wrong with those first three or four Cross books. They're why he became a household name, before the franchise machine fully took over.