As far as comparing water borne amenities at John Pennekamp and Bahia Honda, there's considerably more diving/snokeling offered at J.P. They have a large glass bottom boat for reef viewing as well as four good size boats for snorkeling, as well as a smaller boat for diving.
Boats at PennekampThey also have 20',22'and 23' rental boats. Whereas unless things have changed Bahia Honda only has one boat for snorkeling. The boat they previously had was a glass bottom boat, but that one has been at Pennekamp for ages - (the concessions are run by the same company).