If you are thinking of going to Kekova by boat from Kas, there are a number that do the tour from the harbour and you can book directly with the captain. They vary a little in what is included but most will include lunch and you will get plenty of time for swimming and relaxing etc.
One boat that I have been with many times is the Batin 2 which will take up to about 12 people, the Captain is 'Garlic' Ali and does a very good job of looking after people. (
http://www.batinboat.co.uk/) (
http://www.facebook.com/pages/Bat%C4%B1n-2-Boat/143692512324848)
There are larger boats which carry more people and consequently prices may be a little lower but they tend to be less personal and there is less flexibilty with the route of the tours.
Be aware that boat trips from Kas are not as cheap as some of the prices I hear being quoted for trips from Fethiye, the competition is much less in Kas and the boats generally tend to be smaller than some that I have seen in Fethiye in recent years.
Alternatively you can go by road to the little town of Üçagiz from where you can hire a small boat that will take you around the archaeological sites.
If you want to go through an agent, as I mentioned earlier there are several who will be happy to help (a few websites below). I have no personal experience of them but it should be pretty easy to organise something quite quickly when you get there. As far as I am aware they all tend to do the same sort of thing for very similar prices. They may either take you by minibus to Üçagiz or use one of the bigger boats from the harbour.
http://www.xanthostravel.com/?lang=enhttp://www.koclartour.com/en/http://www.kas-travel.com/eng/There is a small tourist information office in the main square down by the harbour, it is located not far from Ataturk's statue, next to the Meydan Restaurant (quite a nice place to eat and people watch).The position of the information office is also shown on the Google map that I provided the link for in my last post.
Hope this helps
Nick