dtol,
I cannot speak for the rest of the Alaska, but in the Sitka area the most reliable source for anchorages are the locals. The questions they tend to have before giving you a recommendation are time of year, size of boat and wind direction. As the wind in this area is such a key issue, where it is blowing from can greatly affect where it is safe and comfortable or where you will be up all night praying for daylight. Harbormasters tend to be a good place to call, many of the commercial fishing people in Alaska travel a great distance from their home ports depending on what fishery is open and they are a tremendous resource as well.
By the way, the easiest way to get on a commercial fisherperson's good side is to either stick a bumper sticker on your vehicle that states something nasty about farmed fish or something nasty about charter boats. Asking a commercial guy for advice while wearing a charter outfit's jacket or hat will often get you the opposite of what you seek!
We just lost a Sitkan this weekend when the wind hit hard and he fell from his 50' sailboat. Even though he had a lifeline, it took his deckhand an hour to get him back on board due to the rough sea and wind. He had come all the way from Cordova and was not far from home.
It is all about the wind in this area!