I log into my Pi remotely and here is how I shut it down:
- Execute the command: sudo shutdown -h now
- Wait until the LEDs stop blinking on the Pi.
- Wait an an additional 5 seconds for good measure (optional).
- Switch off the powerstrip that the Pi power supply is plugged into.
Since I use a remote display, I don't necessarily see the final output of the Pi in the command window, which is why I use the activity lights. The non-blinking state of the LEDs is not an absolute indication of a complete successful shutdown but it has worked well enough for me. HTH