Play it by ear, but if time is getting short, then I would vote for the cab. I would vote for the cab anyways, but that's another story. I don't like the subway/train hassle to kennedy, it just takes forever, it will be getting near rush hour, you will be dressed all nice, and have a bag, and the last thing you want to to be packed in a tiny area with a bunch of people.
Save that for when you get to the Freddies.
If you were to do the train/subway thing to get there, hopstop.com (a good source for subway directions, getting better all the time) says (the numbers at the end of each line is travel time):
Suggested Route Time
Start out going on 150th St towards Southern Pky 1.3
Entrance near intersection of 150th St and North Conduit Ave 2.0
Take the JFK AirTrain from John F Kennedy Airport station heading to Jamaica Stati 2.5
Get off at Sutphin/Jamaica Station 6.9
Transfer
Take the E train from Sutphin Blvd - Archer Av station heading Downtown 5.0
Pass Jamaica - Van Wyck 2.0
Pass Union Turnpike - Kew Gardens 3.5
Pass 71 - Continental Avs - Forest Hills 2.8
Pass Roosevelt Av - Jackson Heights 8.2
Pass Queens Plaza 6.7
Pass 23 Street (Ely Avenue) 1.8
Get off at Lexington - 3 Avenues 4.4
Transfer 4.0
Take the 6 train from 51 Street station heading Downtown 5.0
Get off at 42 Street - Grand Central 1.9
Exit 42 Street - Grand Central station 2.0
Total travel time 59 mins
And for your return:
Entrance near intersection of West 42nd St and 7th Ave 2.0
Take the R train from 42 Street - Times Sq station heading Uptown 5.0
Pass 49 Street 1.9
Pass 57 Street 1.8
Pass 5 Avenue 1.7
Pass Lexington Av 1.5
Get off at Queens Plaza 5.3
Transfer
Take the E train from Queens Plaza station heading Uptown 5.0
Pass Roosevelt Av - Jackson Heights 6.7
Pass 71 - Continental Avs - Forest Hills 8.2
Pass Union Turnpike - Kew Gardens 2.8
Pass Jamaica - Van Wyck 3.5
Get off at Sutphin Blvd - Archer Av 2.0
Transfer
Take the JFK AirTrain from Sutphin/Jamaica Station station heading to JFK Airport 2.5
Get off at John F Kennedy Airport 6.9
Exit John F Kennedy Airport station 2.0
Exit near intersection of 150th St and North Conduit Ave
Start out going on 150th St towards Southern Pky 1.3
Total travel time 1 hour 0 mins
At that hour of the morning the trains (subways for those who prefer that) may be a few minutes apart, so i would consider the hour to be a best shot thing.
If you wanted to get to Penn Station (Walk, Cab, or whatever) at that hour of the morning, the LIRR trains depart at (saturday mornings)
5:10
5:29
6:05
6:14
6:39
And take about 20-25 minutes to jamacia station, then the airtrain from there is every 15 minutes or less depending on the time of day, then it's like 16 minutes to the furtherest terminal.
Full details over at
http://www.panynj.gov/airtrain/