My husband and I did the same thing last year... We took a cruise to Alaska and then spent an extra (3) days in Vancouver... We also rented a car and went to Seattle as well.
We stayed at the Sandman Hotel in downtown Van. The price was very affordable compared to everything else in the area, and it was close to everything. My favourite thing about Vancouver was Stanley Park. If you guys are nature lovers you will absolutely LOVE Stanley park. Spanish Banks... Which is like a beach area is also very nice. Especially if its sunny and warm.