Any suggestions on a quality fishing experience while on an Alaskan cruise? Suggestions on who to use? Best way to book a guide? Which are the best ports to book a fishing charter from? I don't want a tourist trap or just a boat ride. I am thinking it best not to book through the cruise line but to call the guide directly.

When are you going? Where will you be in port? Salmon, halibut, or bottom fish? Does it matter? How much time will you have? Salmon fishing is a matter of timing, if the fish are in you are probably going to catch some. Bottom fishing for rockfish and halibut can be a little more reliable as most guides have a honey hole or two. Try to pin something down as soon as you can. It can be very difficult to find someone with an opening even months in advance. Whatever you decide Alaska is an awesome place to fish and be out on the water. Good luck!

Ketchikan has alot of cruise ship charters, in part because the fishing grounds are just a few minutes from the docks.

I'd recommend Bruce Johnstone, True Alaskan Charters http://www.truealaskancharters.com/ I know Bruce, and he's a stand-up guy. Great customer service and rapport, and he'll do his damndest to put you on fish (though some days they aint biting)

We are looking at next summer but nothing definite yet. Just starting to look into it. Thanks for the info.

I would suggest flying up there and seeing what you want and fishing without a time frame. AK has so much to offer, a cruise is cutting yourself short.

If doing a cruise I would stick with cruise recommendations and book through cruise. If you have issue or miss boat etc.... the cruise lines will help as you booked through them. If you go outside of cruise line you are on your own if issues arise.
If you just want to fish and book your own options take diamond10x's suggestion and just fly up for trip.
Either way good luck and have great time.