I recommend you to read the following post: AngularJS: "Controller as" or "$scope"?
It describes very well the advantages of using "Controller as" to expose variables over "$scope".
I know you asked specifically about methods and not variables, but I think that it's better to stick to one technique and be consistent with it.
So for my opinion, because of the variables issue discussed in the post, it's better to just use the "Controller as" technique and also apply it to the methods.