SCC is a nice place, but, dang, their bike prices are high. I've bought clothes there, but the bike prices border on ridiculous. I despise Jax near the pier. They provided me with my single worst bike experience and I'll never return.
Huntington Beach Bikes on Edinger and Springdale is a pretty chilled out little shop. Not the biggest supply on hand, but a lot of help and very personable.
If you're buying your first bike and on a budget, you could do a lot worse than Performance on Warner. There's a bunch of people who will cry heresy, but if I had $1k or less to buy a bike it would be their house brand or a Schwinn with good components as opposed to a low end 'name' (probably built at the same factory) with lesser components.
That's just me.