If it's a question, then 'How long will it be' [before you graduate?]
If it's in a sentence then you could say 'I don't know how long it will be before I graduate'.....so it depends on the context, but as Andrew says, it is most likely you are asking a question and therefore it would be 'How long will it be...?'
You might want to write a complete question as it also could be 'How long is it?' etc
thanks! :)