We rented a 3-bdrm condo on Mission Bay when we went last October. We were very happy with the company we found through VRBO and the condo we got was just what was promised. I believe this company also has other units of 1 and 2 bedrooms in the San Diego area. I'm not sure if I'm allowed to post a company's name (it's a no-no on another travel board I frequent) but if you PM me I can give you the name.
I had varying experiences dealing with people from VRBO listings, from professional companies to individuals who couldn't be bothered to return my calls or e-mails even after they said they wanted to rent to me. There are literally hundreds of listings in the area, so I narrowed by general location (we wanted Mission Beach or Bay), sleeping 6 and in what bed configuration, whether the unit had dedicated parking (very important), and of course price. I ended up sending inquiries to about 10 places and then following up with specific questions as I heard back.
If you are going in the off-season (i.e. not summer or holidays) many places will rent for a partial week, but high season will likely require a full week's rental.
PM me for the name or more specific questions,
PHXscuba