Apple - After using `networksetup -setdnsservers Wi-Fi "" ""` how do I clear them?

If you're concerned only about cleaning DNS entries, the command help gives you instructions what to do:

Usage: networksetup -setdnsservers <networkservice> <dns1> [dns2] [...]
       Set the <networkservice> DNS servers to <dns1> [dns2] [...]. Any 
       number of dns servers can be specified. Specify "Empty" for <dns1> 
       to clear all DNS entries.

In my case

sudo networksetup -setdnsservers Wi-Fi "Empty"

  • Create a new network service with the respective interface (e.g. en1 = AirPort):

    sudo networksetup -createnetworkservice Wi-Fi2 en1

  • Remove the one with the custom DNS settings:

    sudo networksetup -removenetworkservice Wi-Fi

  • Rename the new network service to the original name:

    sudo networksetup -renamenetworkservice Wi-Fi2 Wi-Fi

In my environment the new service fetched DHCP and its new settings automatically. You may have to set it with sudo networksetup -setdhcp Wi-Fi explicitly or look at the DHCP response for the interface and parse the supplied DNS ip(s) with ipconfig getpacket en1 though.