Instead of Hyperdia, I would strongly recommend using Google Maps for transit directions. You can plan a journey from exact point to exact point, and it will consider all of the available station and transfer options, including walking time. Google also has the limousine bus timetables loaded and will show you bus options alongside train options.

Here's an example of directions from NRT T1 to the Sheraton Miyako - check out the "Schedule Explorer" for a nice visual representation of the different options and how long they would take.