I read that via Philippine Airlines (PAL), you CAN book a very affordable flight. This guy spent only Php 1757 for a two-way ticket. Impressive!
But aside from PAL and Skyjet Air, you can also book Batanes flights via SkyPasada.com. I learned this while waiting for my aunt at the airport in Tuguegarao. The lady, a receptionist (?) of the Civil Aviation Authority, said a one-way ticket costs around Php5,000. That price tag is probably a Tuguegarao-Basco flight.
According to Skypasada.com’s route map, you can choose from the following departure locations: Laoag, Tuguegarao, and Manila.
Here’s an image of a Skypasada.com plane.