You won't be able to upgrade online as VS won't have any control over the ticket. Once you can check-in online, control will pass to Virgin, so any upgrades will have to be done at the airport.

I assume you are upgrading from Economy? In the past I have been quoted £200 (or the equivalent USD amount) to go up to Premium, and £750 to go from Premium to Upper. Then again others have reported much better/worse prices so yours may vary.

It will all depend on availability on the day of course, PE and Upper are popular on the JFK routes.