You are best off buying screws for these pieces from a parts dealer.
If you want them in bulk, try Ted the screw guy. He sets up in the orange hall, along the wall where all the entry doors are located.
He also sells mail order (not aware on any web site).
Currently Ted gets one dollar per dozen for plain, commonly used screws such as these. His shipping is currently a flat four dollars per order
The screws for Postwar Lionel F3's and 6464 boxcars are not common hardware that you will find in a hardware store.
As the original poster noted the F3 uses a flat head type "Z" screw, #4 by 3/8.
The original postwar 6464 boxcars used a Rec. flat head type "Z" screw #4 by 3/8.
The difference is in the design of the threads.
You probably could use common hardware store stuff, but risk damaging the threaded holes in which they go.
Also, the odds are that the screws you find will be plated. Ted's screws are black (where appropriate), as were most of the orginal screws Lionel used.
Here are Ted's descriptions to order by:
"6464 boxcar body mtg screw"
"F3 front cab mtg. Screw"