Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Surabaya to Machu Picchu as you normally would.
For a flight from Surabaya to Machu Picchu, you will be flying from Juanda. Surabaya Juanda (SUB) is just 15.0 km from the centre of the city. Juanda is the only Surabaya airport and it handles 0 outbound flights to Machu Picchu per day. 0 airlines have flights to Machu Picchu from Surabaya Juanda on a regular basis.