Well, if the original array still exists, just use the in_array() function on that array instead of the imploded string. But if all you have is the string for some reason, then either explode() it back into an array to use in_array(), or else you could use preg_match() something like:
if(preg_match('/\b' . preg_quote($value) . '\b/', $comma_separated))
{
// it's in there
}