Flying ANC - JFK next year.

Flying ANC - JFK next year. The most effective arrangement would be via Alaskan/Delta. I am a QF Silver and a VA Gold member. The flight ANC - SEA is operated by Alaskan, and SEA - JFK is operated by delta. I can book it through either website (Alaskan or Delta) but my question is which would give me best milage in terms of collecting points? If I book it through DL, which is around $40 cheaper will I not accrue VA points from ANC - SEA.

I should also add that either website I book it under will give me the same PNR. 

Have you looked at booking with VX (Virgin America)?

Yes but Virgin America tickets aren't on sale as they are a seasonal service (US Summer Only). And also they leave at around midnight which is bad timing as I need to leave mid afternoon :(

If you are booking a flight say with Qantas, I would book the ANC- JFK as a part of your international ticket under QF code and get points and status credits  at QF's rates. It would mean travelling through LAX.

I am flying OOL - SYD - LAX - YVC then JFK - LAX - BNE. I wanted to book via QF but they don't service Anchorage. 

QF has OOL-ANC fares with applicable routings via SFO, LAX, DFW, and HNL on AS and VX (depending on the transfer city).

But obviously none via YVC or JFK ortherwise you would have been able to get at least part of your flights to/out of ANC.

Did you check AA? They service ANC, and the miles can go to your QF account.