Stockholm harbourfront land is too expensive to house hotels, for the most part. The only one I can think of that's really facing water is the Sheraton Stockholm in Tegelbacken, right by the Centralen train station and bus station.


sheratonstockholm.com

The other nice hotels downtown are the Nordic Ice and its twin the Nordic Sea hotel, all nearby.

But if you want a nicer area around than just lots of highway overpasses and train tracks, I recommend instead the Crystal Plaza on Birger Jarlsgatan. excellencehotels.se