Chwinga are original to Tomb of Annihilation.
The chwinga are a new invention of D&D 5th edition. They don't appear in earlier editions of D&D, and I can't find any creature by that name at Google Books or the Internet Archive's library. The creature's inspiration would be a matter of speculation; we might not be certain without asking the book's designers.
However, I did find the term chwinga in some old texts, where it refers to an item or concept in Australian aboriginal beliefs.
Encyclopedia Britannica Vol.19 says:
The sacred as the secret. The literal sense of the term chwinga, applied by the Central Australians to their sacred objects, and likewise used more abstractly to denote mystic power, as when a man is said to be “full of churinga,” is “secret,” and is symptomatic of the esotericism that is a striking mark of Australian, and indeed of all primitive, religion, with its insistence on initiation, its exclusion of women, and its strictly enforced reticence concerning traditional lore and proceedings.
The Native Tribes of Central Australia mentions chwinga or "churinga" as part of the beliefs of the Arunta or Arrernte people. A churinga is a sacred object or totem, though the word itself may also mean "sacred". Lectures On The Religion Of The Semites The Fundamental Institutions (1927), p. 568 and 635, describe churinga as sacred stones.
Wikipedia has an article on these sacred objects, spelled also tjurunga. The article describes that magical powers might be attributed to tjurunga, and that they are held with such secrecy that only certain people are allowed to view it.
D&D's chwinga can turn into long, thin stones when they die; have a connection to stone, grant benefits to humans, are highly secretive, and are often depicted as dark-skinned. In that regard, they resemble the sacred stones of Arrernte belief. However, they may also draw from other myths: melding into stone is a trait of dwarves from Norse myth, being secretive and giving gifts to humans are traits shared with the Japanese korobokuru, and the notion of little men who use magic and live in the woods appears in English folklore.