The main struggle in a story occurs internally or externally

It depends on the book, it could be either. 

It can be either. That is because some characters struggle through internal conflict. Internal conflict is conflict with the characters self/in his own mind. Making a hard decision may be an internal conflict.
Another conflict can be external conflict. That is also hard because many characters cannot control something else. External conflict is conflict that is around a character. Something other than the character. An example is a conflict with the weather, (hurricanes, tornado's). 

In my opinion, I think external conflict is a main struggle because that character cannot stop that thing easily. In an internal conflict, many control their thoughts/feelings.