The most comfortable way to travel between the Airport and Peniche is probably by taxi (costs around 100€). Please order the Taxi from Peniche before arrival, because a taxi driver in Lisbon will charge you at least 125€, more likely 150.
Fernando runs Berlenga Grande taxi service. He speaks perfect English and even got a 9 seat Mercedes van. He can pick you up at the airport. Just tell him you are staying with Sebastian of Surfguiding Peniche. His number is +351 967 123 500.
To trip from Peniche bus terminal to Baleal should be around €7 (at night 10€+)
Here are some more taxi numbers:
Tel.: +351- 966301396 or +351 – 967004862