If you want to get a really unique view of Vancouver and the surrounding bodies of water, drive across the Lion's Gate Bridge and up to Cypress Bowl / Provincial Park. On the twisty / winding paved road to the top, there is a scenic overlook. I think this is the best view of the city.
I really enjoyed my time shooting in Vancouver - it's one of the most photogenic places I have ever been. Here is my shot list of the top 5 places (in my opinion) for photographers:
1) Stanley Park (day or night). Be sure to shoot the skyline, the totems, visit the zoo, and enjoy
2) Drive up to Cleveland Dam. There is a beautiful park there complete with hiking trails, views of the two "Lions", and an awesome reservoir.
3) Drive up to Cypress and stop off at the scenic overlook. Bring your longest lens - on a clear day you will be rewarded with some spectacular views of the city.
4) Shoot the Lion's Gate Bridge and the Vancouver skyline from West Vancouver.
5) Head on over to the Chinese Gardens and Chinatown. Vancouver has long been home to many immigrants. This is one reason why you can find so much diversity in architecture, parks, churches, and the people.
If you are efficient, you can shoot all of these in two days. I did not have a chance to shoot inside the city as much (there are many great parks, churches, and the famous Gastown area). I'm sure those are awesome as well - I will get them next time.
What are your favorite places in Vancouver?
digcam.meetup.com/cities/ca/bc/vancouver/ - This is a great resource for photographers in Vancouver. If you are looking for classes, photowalks, or just tips on where to shoot - check it out.