Originally Posted by
sdsearch
Using hyperdia.com, I enter HIBASHINIHOMBASHI as my departure, OTSUKI as my arrival, and 12:00 pm on a random date in March (because this site too won't show me April yet!). It shows me a 1-connection route
If you're counting that as 1 stop, then the route from Shinjuku is non-stop. When you wrote "I have to change trains anyway", I assumed that you were describing the journey from Narita Airport to Otsuki. Hence my comment that the "change" was your overnight stop.
The stations at Shinjuku are indeed separate stations.