IMO the best way to do JetBlue T5 and Centurion T4 is to basically use the walkway between terminals.

If you want to save time, just head straight to T4 with your luggage and then head to T5 to check-in/board.
If you have extra, extra time you can always check your luggage at T5 and then go to T4 and then go back to T5.

I have Pre-Check and Clear so the lines really were not bad between the 2.

The AirTrain was hit or miss last time I was there and there was only 1 track in use. Not to mention the positioning of the T5 stop means you have to walk almost the equivalent distance of going from T4 to T5 by ground anyways...