Resolution:
You just have to upgrade to EMS 4.1 on the server and do the following.

#1Property to set the Reconnect attempts:-

Use the property com.tibco.tibjms.reconnect.attempts to set the reconnect attempts in bwengine.tra and designer.tra

eg)

java.property.com.tibco.tibjms.reconnect.attempts 20,5000  (20 reconnect attempts in intervals of 5 seconds)

#2Classpath adjustment:-
Copy the tibjms.jar  from ..ems/clients/java directory to the client machine
Adjust the classpath in bwengine.tra and designer.tra by including the "tibjms.jar" ahead of the other jars.

eg) tibco.env.STD_EXT_CP C:/tibco/JMS/clients/java/tibjms.jar;[Others]

#3 Setting Multiple JMS URLs:-

Multiple URLs can be specified in the UI within the URL field separated by comma.The URLs can also be set in a GlobalVariable and the GlobalVariable can be referenced in the field. If only one server is used and if reconnect needs to be enabled, then the same server URL can be repeated twice.

Please note that the above settings are required for the AE plugin( Adapter Subscriber, Publish to Adapter etc..) activities using JMS as transport. For the JMS plugin activities like JMS Queue receiver etc.. you do not need to do any settings for reconnection.