I found two sources willing to speculate on possible origins of the word, although it would be reasonable to say that the origin is widely considered uncertain.
From Green's Dictionary of Slang:
? Chinook jargon copasenee, everything is satisfactory, esp. as orig. used on the waterways of Washington state. Other etys. include: (i) the painfully contrived phr. the cop is on the settee, i.e. the cop is not paying attention, which elided into copacetic and was supposedly used as such by US hoodlums; (ii) a word presumed to be Ital. but otherwise unknown; (iii) Fr. coupersetique, f. couper, to strike; thus striking or worth a strike; (iv) the Yid. phr. hakol b’seder, all is in order or, earlier, kol b’tzedek, all with justice. Note that HDAS dismisses all these and states ‘ety. unknown’
In an article syndicated in 1994, Evan Morris offers similar speculation:
Theories as to the origin of "copacetic" are literally all over the map. Some authorities trace it to an Italian word "copissettic," supposedly meaning "excellent," but others point to a Creole-French word, "coupersetique," or "able to be coped with." My preference is for the Hebrew connection, from the phrase "kol ba seder," meaning "all in order." There remains the question, of course, of how a Hebrew phrase came to be current in American black English. The most likely explanation is that a Jewish shopkeeper, when asked "How's it going?" might well reply with "kol ba seder," and that the phrase was picked up in phonetic form as "copacetic" by his customers. Am I sure that it happened this way? No, but it's a lot more fun than "origin unknown" isn't it?
I certainly wouldn't put a great deal of faith in the speculative conclusion Morris comes to, but it's worth noting that the three most "popular" theories appear to be the Italian, French Creole, and Hebrew possibilities, but the Chinook jargon possibility posited by GDoS appears to be a strong contender.