If you mean best prestige class in terms of fit, then the War Priest is fine. If you mean best as in most effective, War Priest is not. You lose 5 levels of spellcasting power.
Best prestige classes for Clerics are Hospitaler, Radiant Servant of Pelor (Dragon magazine), and the Doomguide (cleric of Kelemvor, in Faiths and Pantheons). All 3 are ridiculously unbalanced, with full spellcasting, undead turning (although the Hospitaler loses 2 levels), extra powers, and no serious penalties. As if the Cleric wasn't powerful enough. Hospitaler even gets Fighter BAB.