We've done the Western cruise with RCI and with Disney just this past June. There are many ways to find excursions with independent companies via the internet. You can do a search on the particular port or whatever activity you wish to do. Another way to find an excursion is by reading posts either here on the DIS Boards or at Cruise Critic.
When looking for excursions to do in Cozumel, I came upon the following site,
http://www.travelnotes.cc/cozumel/tours/jeep.html thought it looked interesting and sent an email to my brother. Funny thing is, he did the same thing and sent it to me! We ended up booking the Jungle Jeep Tour and I have to say it was probably one of the best excursions I have ever done! Our three boys all said "It was better than Indiana Jones"!! Both my dh and my brother shared driving one of the jeeps. We did pass one of the cruise ship excursions and there had to be 15+ jeeps. We only had two jeeps which made for a more personable tour.
My brother found Eagle Ray Divers after doing an internet search
www.eagleraydivers.com and, after reading RellingTwin's post, we decided to book the 3-reef snorkel tour this past June. All I can say was it was fabulous. We say so many different kinds of fish and lunch was awesome.
As for meeting up with the guide, we were given specific instructions on where to go and what time to time them for both of the above tours. We had no problems whatsoever. Anyway, I hope this helps!