Conrad Tokyo is nice, and I once got an amazing upgrade from their base room to an executive suite w/ 1.5 baths (it was right after Christmas last year). I agree that 80k/night is a bit steep, but it's a nice hotel... 48k for Hilton in Shinjuku seems fair.

Anyhow, have you considered Hilton Tokyo Odaiba (former JAL/Nikko Odaiba--not to be confused w/ Grand Nikko Odaiba)? I just booked a room for 39k/night and I find it to be generally a better hotel than the Hilton in Shinjuku. The rooms are bigger, the water view is certainly amazing, and the property is overall quite a bit nicer (the lounge is far nicer than the one in Shinjuku). Perhaps more importantly, I find the service at Hilton Odaiba to be far superior and more "typically Japanese." Lately, I have noticed some inconsistencies in the quality of staff at Hilton in Shinjuku, so I have been shifting my business to Odaiba gradually.

Odaiba offers a lot in terms of shopping and restaurants. The location is a bit tricky, though, if you have to go to the west side of Tokyo (Shinjuku, Ikebukuro, Shibuya, etc.), but access to eastern Tokyo (e.g., Shinbashi, Tokyo, Ginza, Asakusa, Shinagawa, Haneda, etc.) is excellent.