In my opinion, Bonefish aren't too hard to catch. You just need to know where to find them because they aren't in every part of the bay. From my experiences in south San Diego Bay, all Bonefish were caught in very shallow water. I'm talking about approximately 5 feet of water. I can literally jump off the boat and my head would still be exposed. The key is to find sandy beaches in the bay and get as close as you can to the shore if fishing from a boat. Try and set up a nice drift so you run right along the shoreline. There you will find them.
As far as bait goes, I've only caught them on Ghost Shrimp, a very effective bait for all types of saltwater species in California. I like to rig Ghost Shrimp on a drop shot rig with a size 4 bait holder style hook and a 1/2 ounce weight. You can also catch Bonefish on fly fishing outfits just like they do on the east coast. You can also use a carolina rig as well.
To ensure a good time, I recommend a light spinning outfit with 4 to 8 pound fluorocarbon line so the fish don't see your line. Make sure your drag is set because they WILL pull hard and fast.
Lastly, make sure you hang on tight! If you have any other questions feel free to ask. Go get em!