I've stayed at the Hyatt Regency Shinjuku a couple times (conferences), chose it for its pool. A little far from the station, as is #1. Just hop a cab instead of walking.
I have used the Cerulean quite a lot the last two years for the service and location, but have opted for the Westin Ebisu for some of my Spring'17 guests (the location in Ebisu is ok, and my experience with other SPG properties around the country has been positive except for one). But I don't usually eat breakfasts in hotels in Tokyo - too many other good options.