Все вышеперечисленные решения не сработали для меня, тогда я нашел это http://myshittycode.com/2014/02/10/java-properly-indenting-xml-string/
Ключ удаляет пробелы с XPath
String xml = "" +
"\n " +
"\nCoco Puff " +
"\n 10 ";
try {
Document document = DocumentBuilderFactory.newInstance()
.newDocumentBuilder()
.parse(new InputSource(new ByteArrayInputStream(xml.getBytes("utf-8"))));
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList nodeList = (NodeList) xPath.evaluate("//text()[normalize-space()='']",
document,
XPathConstants.NODESET);
for (int i = 0; i < nodeList.getLength(); ++i) {
Node node = nodeList.item(i);
node.getParentNode().removeChild(node);
}
Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StringWriter stringWriter = new StringWriter();
StreamResult streamResult = new StreamResult(stringWriter);
transformer.transform(new DOMSource(document), streamResult);
System.out.println(stringWriter.toString());
}
catch (Exception e) {
e.printStackTrace();
}