The best replacement for flagella is flagellum.

The best alternatives to flagella are rated as following:
★★★★★  flagellum
★★★★  cilia
★★★  pili
★★  cilia function
★  cillia
★  cilla
★  eukaryotic flagella
★  fimbriae
★  prokaryotic flagella
★  axial filaments
  endoflagella
  no flagella
  peritrichous flagella

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

Other search terms related to flagella and their ratings are:
★★★★★ eukaryotic flagella
You have in mind a companion for flagella and it is not yet here? Propose!



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