The main difference is certainly the fact that JBoss is an application server and supports the full Java EE stack, while Tomcat is a servlet engine and supports only a small fraction of the APIs which are defined in Java EE.
So, your main criteria should be: Which APIs (Frontend, Business Logic, Persistence, Third-Party, ...) do you need?
You should not make this an easy decision. The fact that you are asking the question indicates that you probably did not have the chance to play around with both and familiarize yourself with the concepts behind Java Enterprise stacks (Java EE vs. Spring vs. DIY).
My advice would be to take the time to evaluate both system - it looks like you are able to use both.
- If you don't need much, you're probably better off with Tomcat, which is small and easy to use, but can be a nightmare to configure if you need advanced functionality.
- JBoss AS comes with a full and mature stack. Everything is just right in place and works fine - the price you'll have to pay is that it way bigger and will take longer to start / stop / redeploy.
But again: That's a serious decision with a high impact on pretty much everything...