If safety is your number one concern, take a cab: $45+tip and toll. That being said, maybe instead of taking the subway at 5am, you can leave a little later, and just take the subway to Penn Station and take a LIRR train to Jamiaca from there. Then, just walk upstairs and take the Airtrain. 930 flight - no checked luggage, get there around 8 to be really, really safe. You can leave your place around 7, I'd say.