Where to pull LED: VCC or GND?
You should check the spec of the IO port. 

If your circuit is like [Vcc --> LED --> resistor --> IO port] the port must be able to sink the current required for your LED. 

If your circuit is [IO port --> LED --> resistor --> GND] then your port needs to be able to source the current required for the LED.

One isn't inherently better than the other. It depends on your design constraints. If Vcc is a much higher voltage than your IO port can reach than the first option won't work (could never shut off the LED). If they both are 3.3V then it shouldn't matter, but check the specs.