If BW is the type of hotel you are thinking, I have stayed at the BW Inner Harbour and would recommend it. The rooms have a small alcove off the corner of the room, doesn't take away from the room itself, with a small table. It's on a treed, residential street. I have stayed on the 7th top floor on the harbour side and at night the lights all around the harbour were pretty attractive. There is another BW I believe, but IMO it is not as appealing location wise as the BW Inner Harbour. I've stayed at the Harbour Towers as well and found that nice. Had a room on one of the higher floors with a full view of the Strait of Juan de Fuca and the Olympic Mountains. That was nice.
I've also stayed at a similar class of hotel, Chateau Victoria, which is on the other side of the harbour and more 'citified" but very convenient for walking everywhere. They have standard room up to about floor 5-6 and suites above that.
From the BW Inner Harbour to the Bay Centre, on the other side of the harbour, is about 1 km and about 15 minutes walking. Such a nice city to walk around in.