Well...in May and June you get into the whole "May Gray", "June Gloom" weather pattern. Along the coast (and even a few miles inland) it is usually cloudy and overcast in the mornings - sometimes it clears in the afternoons and sometimes it doesn't. Temps are usually around 70-75 on the coast. It doesn't rain, but it's gloomy. Nice for the Zoo, not so nice for Sea World or the beach. Sometimes we'll get a stretch of several days where it's sunny all day, but it's not predictable at all. Should be nice at the Wild Animal Park - if you're going there, then May is better than June since it'll be a little bit cooler - it gets HOT at the Wild Animal Park even when it's cool along the coast.
As far as crowds go, they shouldn't be too bad mid-week in May or early June (before school gets out here).