My best stay has been at the Conrad Hotel overlooking Hamarikyu gardens in Tokyo. The room was beautiful, with a spectacular bay view, and a large bath tub next to tall windows so I could enjoy the scenery while bathing. It was a great experience, one of the perks I got from Amex. Check-in was 11 am, and check-out was 4 pm. But at $790 per night, it wasn't cheap.
My favorite ryokan is here:
湯河原温泉露天風呂、料亭旅館 | ゆば懐石山翠楼 I stayed here for a couple nights last summer, the rate for 2 people per night was about 80,000 yen ($1600 for the weekend). But the room had an onsen tub on the balcony, with a breathtaking view of the valley, and the dinner was the best that I have had since I moved to Japan.