The Javadoc for the WebSphere MQ JMS classes can be found here. What you want to do is to create an instance of the com.ibm.mq.jms.MQConnectionFactory, com.ibm.mq.jms.MQQueueConnectionFactory or com.ibm.mq.jms.MQTopicConnectionFactory. Once you have an instance you can configure it using the various setters and then call one of the createConnection methods. A simple example would be:
MQConnectionFactory factory = new MQConnectionFactory();
factory.setQueueManager("myQmgr");
factory.setTransportType(WMQConstants.WMQ_CM_BINDINGS);
Connection conn = factory.createConnection();
Session session = conn.createSession(false, Session.AUTO_ACKNOWLEDGE);
Queue q = session.createQueue("myQ");
TextMessage msg = session.createTextMessage();
msg.setText("My message body");
MessageProducer sender = session.createProducer(q);