http://www.illabalear.com/INGLES/Iindex.html
This is the main boat trip company who operate from Cala Bona, there is another company who use the Porto Cristo Cat but I cannot lay my hands on their website at the moment.
I can highly recommend these boat trips, they are brilliant.
I cannot help you with other trips as we always have a hire car and will again in June.
There is a tourist information shop in Cala Millor which is just a short walk from Cala Bona.

Dara

edit: just found that web address: http://www.crucerosbarcelo.com/indexi.html

There are a few tour shops dotted around both resorts, there's one on the front in Cala Bona next to Supermarket Paula (near to the Hotel Alicia) it's called I.PUNKT TOURS....never used them but they've been selling excursions in both resorts for a canny few years so they must be doing something right.

For boat tours we always book at kiost at Cala Bona harbour and use Illa Balear sea cats...we took boat up to Cala Ratjada last year and came back a few hours later...cost €18 per adult and €9 per child...only had to pay for 2 kids as 3rd went free (special offer)....we went from Cala Millor jetty (they have a kiosk there too) up to Cala Ratjada calling in at Costa de los Pinos and Canyamel, return journey missed out Cala Millor and went straight to Sa Coma before dropping us back off in Cala Millor so we got our money's worth I would say.

They do 'pirate' cruises.....we did that one in 2008 and think it was a special offer of around €20 for an adult and we were out for AGES and went down to Porto Cristo and Cala Romantica, looked at sea caves etc

Just found I.PUNKT TOURS website

http://www.i-punkttours.com/ipunkt-excursions.htm

and to add if you are thinking about doing the Auto Safari in Sa Coma...give it a wide berth as it's awful!