What is the best way to secure a set of folding attic stairs?
If you are not opposed to replacing the ladder, they do make attic ladders with integrated locks (i.e. Fakro Insulated Wood Attic Stair Ladder.  It looks like you need a special "handle" mounted on a 3 foot pole to lock and unlock the latch.  I'm not sure if these locks can be accessed from the top, but it is at least worth looking at.

If you prefer to leave the door in place, you could attempt to retrofit a remote control deadbolt to the door.  Depending on the style of door and the way it is installed, this may or may not be possible.