Best Western Island Palms on Shelter Island is awesome. Right on a marina with some fantastic views. A few pools and an awesome restaurant and outdoor patio for breakfasts etc. Was very affordable when we were there in December and were upgraded for free.
https://www.tripadvisor.ca/Hotel_Rev...alifornia.html
Youre with family, but even so, San Diego has some of the best microbreweries in the US.