Here is the language from the EO issued by Gov. Cuomo (as well as by the govs. of NJ & CT). I sure would not want to argue as my defense before a judge in any of the three states that flying LAX-BOS-JFK isn't flying from California.
All travelers entering New York from a state with a positive test rate higher than 10 per 100,000 residents, or higher than a 10% test positivity rate, over a seven day rolling average, will be required to quarantine for a period of 14 days consistent with Department of Health regulations for quarantine.