<?php

$str = "The man drove in his car.Then <strong>the man walked to the boat.</strong>"; 
$keywords = array('boat','car');
$p = implode('|', array_map('preg_quote', $keywords));
$result = preg_replace("#<strong>.*?<\/strong>(*SKIP)(*FAIL)|\b($p)\b#i", "gokart", $str);
echo $result;