Okay, so what you call “internal annotations” are absolutely not annotations according to the Java languages. These are comments or javadoc.
In our API, you can access them through the modifiers() of some elements from the AST (such as MethodThree). However, the simplest way is to retrieve directly from any syntax token, using the trivias() method. You can also decide to use a SubscriptionVisitor, and register to the TRIVIA kind.