The best replacement for morpheme is phoneme.

The best alternatives to morpheme are rated as following:
★★★★★  phoneme
★★  allomorph
★  grapheme
★  syllable
★  bound morpheme
★  morph
★  utterance
  free morpheme
  grammatical morpheme

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No companions for morpheme have been suggested so far.
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Google Trends

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morpheme
phoneme
allomorph