San Diego is located in a desert region, which means that unless it has rained recently (it is expected to rain from time to time from November through March), there will be flowers only in irrigated parks.
If you have the opportunity to go look for flowers in January through March (or later if it rained a lot), then parks like the Mission Trails Regional Parks are a good bet, especially 2-3 years after a fire. The book Afoot and Afield in San Diego County is a great resource to find out where to go.
For an easy access to (mostly not-so wild) flowers, look for flower season activities: In addition to special events in the Balboa Park, they suggest a trip to the Flower Fields (tm) in Carlsbad, which is about a 1h drive from San Diego, a visit of floral art in La Jolla or on Coronado Island, and finally, a 2.5h trip to the Anza Borrego State Park, to see flowers in the desert - this trip is worth it even if you miss the flowers.
EDIT If Antelope Valley (just north of LA) isn't too far, it's a great place to see California's state flower. The number of poppies you can see varies from year to year, but if you hit a good one, it's a sight you'll never forget.