Option 1.) Set as input, and use an external resistor to pull it to VCC or GND.
Option 2.) Leave them unconnected on the PCB, and through software make them all inputs and enable the input pullups. This is less expensive than 1.) in terms of board area and cost, but depending on your application can pose problems on startup if you're in a noisy environment as some pins default to hi-z.
Option 3.) Leave unconnected on the PCB, and drive as an output to VCC or GND. Disadvantage is that it can lead to a short if something touches it.
Don't tie a pin directly to VCC or GND because that leaves the possibility of shorts during development if you accidentally set that pin to an output.
Leaving an input pin floating is typically not a good idea; noise can cause it to flip states a lot and that can burn power in the cpu circuitry connected to it.