Several of the theme parks have booking agencies scattered around - for example in the Modelo shopping centre (about a mile from Sao Joao) Zoomarine has its own little shop and there are also there agencies offering bookings for almost everything it seems. You can even go shopping while you are there!

Even my local paper shop sells tickets for various attractions and trips.

Suggest you spend some time first couple of days getting these sorted.

Shouldn't be too much trouble.

There's a tour agency - think it's called 'The Ticket Shop' or something like that, in a square in front of Vila Nova apartments in Sao Joao (top end of the strip) which does trips to just about everywhere.(Someone told us they were the cheapest they had found in the area although can't vouch for that!), and their pick up point is close by on the main road.