Every winter and spring, from mid-December to April, nature fans from San Diego are able to view the annual Gray Whale migration. Thousands of Gray Whales move along the West Coast to reach the warm lagoons of Mexico. The goal of this 10,000 km trek is breeding and calving. After a month "vacation" in Mexico, they return north to their feeding grounds in the Bering Strait of Alaska. So if you want to see females with calves, go late in the season as they head back with their newborns.
Besides the famous gray whale season, San Diego sees another migration of blue whales. It takes place in summer and early fall, namely mid-June to September. So whale watching is in the area is available nearly all year round.
During the whale watching season, there are plenty of ways to see the migration in San Diego and you don't have to go far. Most whale watching tours are quite short, and chances to see whales are quite high. Cruises include all kinds of boats and rafts. You can even take a tour on a kayak and paddle as close to whales, seals, and sea lions as possible.
You can also see whales from the shoreline. Best viewing spots are located in La Jolla, Scripps Park, Torrey Pines State Reserve, the Birch Aquarium.