The physicist who named the particle apparently liked to come up with nonsense words in his head. Later, when trying to decide the spelling, he came across a quote by James Joyce and spelled it “Quark”. Unfortunately, the particle rhymes with fork, while the german cheese rhymes with Mark.

According to his own account he was in the habit of using names like “squeak” and “squork” for peculiar objects, and “quork” (rhyming with pork) came out at the time. Some months later, he came across a line from Joyce’s Finnegans Wake:

Three quarks for Muster Mark! Sure he has not got much of a bark And sure any he has it’s all beside the mark.

The line struck him as appropriate, since the hypothetical particles came in threes, and he adopted Joyce’s spelling for his “quork.” Joyce clearly meant quark to rhyme with Mark, bark, park, and so forth, but Gell-Mann worked out a rationale for his own pronunciation based on the vowel of the word quart: he told researchers at the Oxford English Dictionary that he imagined Joyce’s line “Three quarks for Muster Mark” to be a variation of a pub owner’s call of “Three quarts for Mister Mark.” Joyce himself apparently was thinking of a German word for a dairy product resembling cottage cheese; it is also used as a synonym for quatsch, meaning “trivial nonsense.”

www.merriam-webster.com/wordplay/quark

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However, there is another interpretation of the quote.

This passage from James Joyce’s Finnegans Wake, part of a scurrilous 13-line poem directed against King Mark, the cuckolded husband in the Tristan legend, has left its mark on modern physics. The poem and the accompanying prose are packed with names of birds and words suggestive of birds, and the poem is a squawk against the king that suggests the cawing of a crow. The word quark comes from the standard English verb quark, meaning “to caw, croak,” and also from the dialectal verb quawk, meaning “to caw, screech like a bird.”

www.ahdictionary.com/word/search.html?q=quark

This sounds very learned and all, but I can’t find that standard English verb in the dictionary.