We've been visiting the Best Western Island Palms Hotel & Marina for the last 3 years. Each time we spent a week in April and every time we came back enchanted with our stay.
Nice rooms, staff is great, breakfast at their restaurant is excellent (although the coffee is not strong enough!) and location is great.
It's hard to find a better deal for a stay in San Diego. It's easy to go everywhere from Shelter Island where it is located if you have a rental car.
We hope to be back again!