To each their own, naturally, but the top contenders would have to be...
Breakers Revenge, Ninja Masters, Matrimelee, Garou, Art of Fighting 3, Real Bout Fatal Fury 2/Special, KOF 98/2002, Kizuna Encounter, Last Blade 2, Samurai Showdown 2/5 Special, and Waku Waku 7.
They're all about different enough as fighters that folks will have their own favorites, or wouldn't compare them. (Someone might also say SVC Chaos, but let's be real, it's not even the best Capcom/SNK crossover.)
Personally I'd say Garou: Mark of the Wolves was the high watermark of Neo Geo fighters, followed closely by KOF 98.