The best replacement for phoneme is allophone.

The best alternatives to phoneme are rated as following:
★★★★★  allophone
★★★★★  morpheme
★★★  phone
★★  grapheme
  syllable
  phonogram
  phonetic
  speech sound

Your alternative for phoneme is not listed? Suggest!
Speaking about phoneme, one probably shouldn't forget about oe.

Other search terms related to phoneme and their ratings are:
★★★★★ oe
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Google Trends

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phoneme
allophone
morpheme