Without access to example text, it's a bit hard to guess what you really need, but the regular expression
(^|\s)example\.com\>
will find example.com where it is preceded by nothing or by whitespace, and followed by a word boundary.  (You could still get a false match on example.com.pk because the period is a word boundary.  Provide better examples in your question if you want better answers.)
If you specifically want to use a lookaround, the neative lookahead you used (as the name implies) specifies what the regex should not match at this point.  So (?!subdomain\.)example trivially matches always, because example is not subdomain. -- the negative lookahead can't not be true.
You might be better served by a lookbehind:
(?<!subdomain\.)example\.com
Demo: https://regex101.com/r/kS1nQ4/3