Hi slam5, welcome to Cruise-Chat! Congratulations on your up-coming cruise to Alaska. Since you won't be in foreign countries, doing your own excursions will not be too much of a problem. I suggest you do research on the internet or through a travel agent. The cruise line excursions contract with local vendors, but of course, get some part of the charges. We normally use the cruise line excursions if we have not been to the port before, but sometimes will just find a vendor and use them.
We've had good luck both ways. One thing I can say for the ship's excursions is that they have checked out the vendor, so normally you will have what is advertised for your tour. You are correct, the ship will not wait if you are not on one of their tours. The chances of being late depend upon, traffic, condition of the equipment, distance you have to travel, time of day you are traveling, accidents, etc. As long as you select reputable companies, you should be fine. Just remember to give yourself plenty of time to get back to the ship and you should have no problems.
Best wishes and have a marvelous cruise!