Well, since you ask ....
Over many cruises we have pretty much evolved a routine. Most of the time we pick an itinerary because there are some special things we want to see on that particular route: The pyramids, the hermitage, Scara Brae, or whatever.
Around 6 to 8 months before sailing we start looking at excursions. Then we check out the ship's excursions. They are always a good starting point and usually include the most wanted attractions. Often there are a number of ship's excursions that appeal to us and we go ahead and book them, especially things like culinary tours or helicopters that may sell out. Otherwise, frankly, we take the attitude that we can cancel if we find something better.
Then I will begin to research independent tours. Frankly I just Google "<name of port> day tours" and get a good idea of what is available beyond what the ship does. Then I visit this board, and other places like TripAdvisor, Frommer's, or Fodor's. I usually check out shoretrips.com and toursbylocals.com. By now my head is spinning with possibilities. Usually from among all this, something rises to the top.
Particularly when it is a single recommended guide we go ahead and get in touch with them. If it is an agency we do the same. A long exchange of emails usually follows, and eventually we wind up with a customized tour that satisfies us. We will put a deposit down with an independent company but don't like to pay in full.
On some rare occassions there will be some good independent driving tour. We did this in Halifax, for example, and Skagway is a very good place. Then we might rent a car and drive ourselves.
It has been VERY rare that we will just get off the ship and hail a taxi. Occasionally we will do this when we have a half day tour booked, and take a short tour with the taxi for the other half day. Or now and then we will have a plan and hail a taxi to take us there.
So normally we wind up with a mix of ship's excursions and independent tours booked well in advance. Now and then a ship's tour will be cancelled and we have to scramble to find something else.
This works great for us. Our latest trip, Australia and Indonesia, is a good example of how it works. Check out our trip report and pictures at Australia and Indonesia Cruise