Originally Posted by
Duke787
If connecting to QR, your best bet is going to be AA.
They won't interline or protect your connection (they stopped doing interlines on separate PNRs even though both are OneWorld) but both QR and AA use T8 at JFK so it should be fairly seamless to get your bag and then walk upstairs to the check-in counters and re-check for the QR flight.
If you fly Delta you'll have to make your way from either T2 or T4 (depending where you flight arrives) over to T8 which is going to take a lot longer than simply going up the escalator as is the case for AA/QR.
Sounds like you already decided on JFK which is the better choice since QR goes out of T5 at ORD which is a pain whether flying DL, UA, or AA for the domestic flight.
Even though AA no longer through-checks bags on separate tickets, it appears that they still protect on separate AA-oneworld tickets in the case of IRROPS.
However, the ATL Airport Wikipedia entry indicates that AA flies ATL-LGA nonstop, but not ATL-JFK. So unless there has been a recent change, if the OP wants to fly AA out of ATL, he will either have to connect somewhere to fly into JFK, or arrange his own ground transportation from LGA to JFK.
Edited to add: This recent post indicates that AA can put an award ticket and a cash ticket on a single PNR, which would allow through-checking of baggage. However, that does not solve the LGA/JFK problem.
https://www.flyertalk.com/forum/32027001-post988.html