As the others said, you use object.equals(otherObject) to compare objects in Java.
But your approach is completely wrong.
Try instead
Set stopWords = new HashSet(Arrays.asList("s", "t", "am",
"is", "are", "was", "were",
"has", "have", "been",
"will", "be", ...));
and then
private void refineWords() {
words.removeAll(stopWords);
}
and you should be done.
Further, note that with your current code you will get a ConcurrentModificationException because you try to change the collection while you're iterating over it.
So if you can't use the abovewords.removeAll(stopWords), then you must instead use the much more verbose Iterator.remove() method:
private void refineWords() {
for (Iterator<String> wordsIterator = words.iterator(); wordsIterator.hasNext(); ) {
String word = wordsIterator.next();
if (stopWords.contains(word)) {
wordsIterator.remove();
}
}
}