The best replacement for vesicle is vacuole.

The best alternatives to vesicle are rated as following:
★★★★★  vacuole
★★★★  bulla
★★★  vesical
★★★  pustule
★★★  papule
★★  blister
★  liposome
★  endosome
★  bullae
  seminiferous tubule
  vesicle

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vesicle
vacuole
bulla