It's not clear to me which of two questions you're asking: (a) Is it always racist to use the word "niggardly"? (b) Can it be racist to use the word "niggardly"? I'd answer "no" to (a). It's not racist, and it's accurate, to describe Ebenezer Scrooge (before his conversion) as a niggardly character. But suppose someone uses "niggardly," perhaps mistakenly thinking that it's related to the N-word, in order to express racial hatred. I think that counts as a racist use of "niggardly," so I'd answer "yes" to (b).
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Is it racist to use the word "niggardly," despite the word not being etymologically related to the notorious N-word?