I recently traveled from India to USA via Dubai. I did not bring a laptop but saw others bringing their laptops along. I understand it is risky, but if you can check-in your laptop in one of the check-in bags, all good!. But for the carry-on ones, here is what Emirates did to save the situation.
Emirates asked the passengers to submit their laptop at a kiosk right at the gate. The staffed packed the Laptop, tagged it and checked-in the laptop package. I am sure they considered the safety measures as it is valuable.
While at the baggage claim on arrival, they set up another kiosk at the destination where you can claim your laptop. I did not hear any case of loss or damage of any passengers of the big A380-800 airplane. This might not be the case for all airlines, but you can verify if they have anything that they can help with.
All said, I found the Customs and Immigration officers quite friendly at JFK. Somebody else might be able to share the severity of the situation. However one of the solution is available to you, in the worst case. Cover the laptop well in clothes and pack it safely in the check-in bag.