stain has 19 distinct synonyms spread across 5 of its 9 senses. Each sense below keeps its own list, because a synonym belongs to a meaning and not to a word: swapping one sense's substitute into another sense's sentence is how a thesaurus makes writing worse. WordNet records no antonym for it — antonymy is a relation between word forms rather than concepts, so it is deliberately sparse.
Counts are distinct word forms across every sense. A synonym that appears under three senses is counted once here and shown three times below, under each sense it belongs to.
a soiled or discolored appearance
“the wine left a dark stain”
(microscopy) a dye or other coloring material that is used in microscopy to make structures visible
a symbol of disgrace or infamy
“And the Lord set a mark upon Cain”
color for microscopic study
“The laboratory worker dyed the specimen”
Synonyms, antonyms and the broader and narrower relations for stain come from Princeton University’s WordNet. Full sources and licences.