There are three lagoons on the Pacific coast of Baja where Gray whales find the optimum conditions for their nurseries. The lagoons are government protected marine parks, and access for whale watching is only allowed on permit basis.
Only motor boats (pangas) with trained guides may be used for whale watching.
Sea kayaking in the lagoons is prohibited during the whale migration, with the exception of Magdalena Bay (the third lagoon).

1) Scammon's lagoon is Baja 's most northern whale watching location (and the closest to the US), about 440 miles South of San Diego, California. Scammon's is also the largest of the three whale watching lagoon; Over 1000 whales have been counted here during the 2002 season.

2) San Ignacio lagoon is about 530 miles South of the border, somewhat smaller, slightly fewer whales.

3) Magdalena Bay, 800 miles from the border, is the last protected lagoon on the Pacific coast of Baja, and the only one where sea kayaking is allowed (as well on permit basis) during the migration of the Gray whales.

Conclusion: The lagoons of the Pacific coast of Baja have the greatest concentration of whales per square mile, but only from mid-December to mid-March, with the numbers peaking in January & February. and only Gray whales.
The Sea of Cortez is blessed, maybe not with such great concentration of whales per square mile, but with a variety of whale species, and high chances that you will see some whale activity practically any time of the year (some species live here all year, see table above).

If Gray whale watching is your main interest, the Pacific lagoons of Baja are the right places during January & February of every year.
If you interest is sea kayaking expeditionary style, in a spectacular marine environment with oportunities of encountering a rich variety of sea life including the true giants of the Earth, the Blue whales, our trips on the Sea of Cortez are the best choice.