Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Surabaya to Bora Bora as you normally would.
For a flight from Surabaya to Bora Bora, you will be flying from Juanda. Surabaya Juanda (SUB) is just 15.0 km from the centre of the city.
This is defined as Surabaya Juanda Airport (SUB) and Vaitape Motu-Mute Airport (BOB). Codes like Vaitape Motu-Mute Airport are often used to just call airports uniquely.