Shorex on any cruise can be done via the ship or by yourself. The best bet in finding something yourself is by using searches, finding companies and most importantly getting word or mouth recommendations from either past clients or from travel journalists/guide books. Generally there will be taxi's and minibuses all wanting your trade/money at the quayside. Often you can find a bargain but that is not always guaranteed. Shop around to find the best deal for both ship shorex and doing it yourself and then base a decision on that. That is what I would do anyway
The one big thing that should always be remembered is that the ship's own tours do guarantee that the ship will not leave without you if the tour runs later than scheduled.....whereas if you go it alone, and you have a breakdown or have left the return journey to the ship too tight and you get caught in traffic, well chances are you will be waving the ship bye-bye from the quayside. So if you do go it alone, give yourself at least an hour-90 mins to get back to the ship before the sail away time.