After 1963 ??? No. In any time post-New York Agreement West Papua's fate is already sealed, except if maybe US would somehow invade and at least managed to acquire eastern part of the country a West Papuan state will may have its chance. That will surely be a world where US involvement in Vietnam being a much less memorable event, btw.
And btw, be carefull of this PC meme about Indonesia=Javanese Empire thingy. Javanese people do have this sheer advantage from being the single largest ethnic group, but they are by no means like Han Chinese in China or Russians, their number is barely 45% of the total population. Also remember that Jakarta is not located in the Javanese part of Java, in fact it is an island in the middle of a sea of Sundanese, and has been THE melting pot of this country since NEI era, besides being THE center of gravity of this country's economy, also since the Dutch era. The later part is actually why Indonesia has been so centralized and not so ethnic-national-principle friendly, though there is also Indonesianism factor. If anything, Indonesia is a Jakartan Empire. Don't worry, for it's not so good either
Anyway, only with pre-New York Agreement PoDs that a West Papuan state can be possible, at least if you want to keep Vietnam within the spot light. The best period is during the War for Independence, which is by the Netherlands government having a more clever design for Eastern Indonesia, by instead of lumping Maluku/South Maluku with the rest of the country, make it a separate state. Assuming minimal butterflies, by the time RIS is dissolved, Maluku/South Maluku remains separate from the Unitarian Republic, thus making a comfortable buffer-state to shield the Dutch presence. However, it will may become so comfortable that West Papua will remain Dutch though....