I rather like the InterContinental Tokyo Bay. It's in a slightly quieter area near the water, and you get some beautiful views on the bay side. Rooms are a good deal larger than the typical Tokyo room. I've gotten some good rates there. Nice walking paths and a park next door. Easy trip from Haneda. There's a train stop out front (Waterfront line) or 10min walk to Hamamasutcho. Main downside is not a ton of restaurants right nearby (<10min walk).

The Prince Sakura Tower is nice, has a courtyard and a boutique hotel feel but it's right next to Shinagawa Station. It's affiliated with Marriott but they seem to keep that on the DL.

Some colleagues like the Courtyard Marriott Ginza but I haven't stayed there. I have stayed at the Courtyard Marriott Tokyo Station and don't really recommend. Rooms were tiny and soulless, minimal windows, not a lot of amenities, really expensive.