shlex to the rescue!
The module shlex will take a string containing the whole shell command and split it up exactly how Popen and check_output expect it. Like this:
import shlex, subprocess
cmd = "/usr/bin/nmap -sn -Pn todd.ns.cloudflare.com --script dns-check-zone --script-args='dns-check-zone.domain=www.macmonster.com'"
args = shlex.split(cmd)
output = subprocess.check_output(args)
When you look at contents of args you'll see:
>>> print args
['/usr/bin/nmap', '-sn', '-Pn', 'todd.ns.cloudflare.com', '--script', 'dns-check-zone', '--script-args=dns-check-zone.domain=www.macmonster.com']
Note that shlex split up the option "--script dns-check-zone" into two tokens. On the other hand it kept "--script-args='dns-check-zone.domain=www.macmonster.com'", but removed the single-quotes.