Is that not is usually the formal choice; keep not after the subject. In a client email: Is that not the final figure? In chat, say isn't that instead.
Is not that is wrong word order. Which register is yours?
Use is that not when the situation is formal and you want to sound deliberate. Usable sentence, client email: Is that not the figure we agreed on? Keeping not after the subject signals careful, formal wording.
Choose isn't that in everyday conversation, where the uncontracted form can read as stiff. Chat message to a colleague: Isn't that the deadline we set? The contraction is the ordinary choice when you're just checking something casually.
Both forms are grammatically correct and mean the same thing, so this is a register choice, not a correctness one. Quick test: if the setting is formal or written, keep not separate; if you'd hesitate to sound stiff, contract it.