Is your flight a codeshare with Hawaiian, Virgin Australia, or Virgin Atlantic? I'd probably choose one of those to accumulate the miles.
You already have a Star Alliance airline so no need to duplicate mileage there.
You stated that you are very unlikely to use Virgin America again so that would be a waste of mileage.


Side note: Did you look at United's P.S. service? It flies from JFK to SFO/LAX. Not all JFK-SFO flights are P.S. but it seems to be a tossup as far as which product is superior ... some favor VX, some favor UA P.S.
United P.S. info: http://www.united.com/web/en-US/cont...mservices.aspx
You can tell it's a P.S. flight when looking at the seat map; no regular economy seats are offered. They use a 757-200, but they've also got non-P.S. 757-200s on the route. Delta will also be adding a similar product on these routes in the next year; I don't know if American will also add a similar offering.

Comparison threads:
http://www.flyertalk.com/forum/unite...n-america.html
http://www.airliners.net/aviation-fo....main/3519001/
http://thepointsguy.com/2012/07/tran...series-united/