I developed a small Java application using EJB3 and JSF. But I want deploy it on Tomcat server (not GlassFish and not in Netbeans IDE it has to be independent of Netbeans).
How can I deploy it on Tomcat?
You can, but it's not meant to happen that way. Tomcat is a servlet-container, and only application servers are required to support EJB.
Tomcat with integrated EJB support is basically TomEE. Replace Tomcat by TomEE. You can keep using the Tomcat server plugin in IDE to manage TomEE.