FeatureCollection geoJsonDocument = featureJSON.readFeatureCollection(myGeoJsonInputStream));
...
Configuration config = new org.geotools.gml3.GMLConfiguration();
Encoder encoder = new Encoder(config);
encoder.getNamespaces().declarePrefix("myorgns", "http://myorg.org");
encoder.setEncoding(StandardCharsets.US_ASCII);
encoder.encode(geoJsonDocument, new QName("http://www.opengis.net/gml", "FeatureCollection"), out);

<gml:FeatureCollection xmlns:sch="http://www.ascc.net/xml/schematron" xmlns:gml="http://www.opengis.net/gml" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:myorgns="http://myorg.org">
<gml:featureMembers>
    <null:feature gml:id="feature-0">
        <gml:boundedBy>
            <gml:Envelope>
                <gml:lowerCorner>3.4686311 51.1304626</gml:lowerCorner>
                <gml:upperCorner>3.4686311 51.1304626</gml:upperCorner>
            </gml:Envelope>
        </gml:boundedBy>
        <null:pk_track>729</null:pk_track>
        <null:time_ISO8601>2017-01-10T05:13:06+01:00</null:time_ISO8601>
        <null:time_epoch>1484021586000</null:time_epoch>
...

Exception in thread "Thread-30" java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 238; The prefix "null" for element "null:feature" is not bound.
at org.geotools.xml.StreamingParser$1.run(StreamingParser.java:248)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 238; The prefix "null" for element "null:feature" is not bound.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
at org.geotools.xml.StreamingParser$1.run(StreamingParser.java:244)
... 1 more