The correct one is ninety-story tall.
Tall is an adjective that modifies building.
Ninety-story is an adverb that modifies tall.
Ninety-tall story doesn't make sense because you are selecting modifiers that qualify how tall the building is, not how tall any story is. Story also is not typically an adjective so it is confusing for that reason too.
Ninety-stories and ninety-stories tall are wrong because only nouns have plural forms in English. Adjectives/adverbs do not. So "ninety-stories" tall sounds like an additional noun for a brief moment until the speaker/reader gets to the word "building" and figures out what you meant.
Incidentally, you could say:
A fire in the ninety-story building could be a problem for firefighters
and that would be OK.