Hi yes there is Brigadoon sea eagle &wildlife trips at Portree also Wild sky trips @place called Carbost and Misty Isle trips at Elgol .

I think the excursions take you to the most famous (popular) sights of Skye - like Old Man of Storr, or Fairie Glen, or Fairy Pool, or Neist Point, etc. I am not sure how accessible these will be from the ship. Most of these attractions are quite far from Portree harbour and usually require driving to the attraction followed by a walk for the last bit. If you have time and the chance to explore Skye (either by yourself / with an excursion) I would highly recommend you do that. The charming town of Portree is quite small and you can see walk around it in an hour.