I thought that the word honcho as in head honcho (big leader / big cheese) came from Japanese. The OED and the Online Etymology Dictionary both say that it comes from the Japanese word 班長 (hanchō) or squad / team leader, and that it was borrowed by American servicemen in Japan and Korea in 1947-1953.
However, according to The Basque History of the World by Mark Kurlansky, which I’m reading at the moment, the word honcho is a version of the Basque word jauntxo /xaunʧo/, a wealthy. powerful, rural landowner – a word with a ironic, negative undertone. From jaun (sir / lord / god). This sounds kind of plausible, though I haven’t found any other sources which make the same claim.
The book is interesting and includes quite a few bits of Basque language, and even some recipes. It is also somewhat biased in favour of the Basques.
Given the evidence, I’m going to have to go with the OED on this one. What’s interesting to me is that the OED also gives it as a transitive verb, and I’ve never heard it that way. That sounds completely awkward.
The Basque etymology seems fishy to me. The transmission from Japanese to American English after the war is plausible and as far as I know, the word is typically American English and doesn’t turn up in other languages.
For the word to come from the Basque jauntxo (which looks to be a diminutive with the palatalised pre-final consonant), you would normally expect it to have passed into (American) English via Spanish. With web searches, I only find “Jauncho”, which seems to appear only as a name, so it seems unlikely that there is or was a Spanish word with the matching sense that would have been borrowed into English.
For the Japanese origin, the American English spelling ‹o› for the [a] speech sound is expected, whereas it’s a bit of a leap from the Basque diphthong to [a] in English. Taking this into account, I think it’s a good guess that the Japanese etymology is the most likely one.