We stayed at the Crowne Plaza, San Pedro, and it was great! You can walk to stores and restaurants (there's a nice one on site), and, if you ask when you check in, you may be able to get a room facing the harbor and see all of the ship's come in!
We've also stayed at the Doubletree, San Pedro. It was also nice, but we didn't find it within walking distance of anything. We thought it was overpriced.