My experience with buses in Nicaragua is that they stop wherever you flag them down. You want the bus going out of town, the buses that stop at the hotel across the street are going into town. I wouldn’t wait in front of the airport, I would go around the corner. Gomez has nice buses.
My best advice is to go to the bus station and the reason is simple: you stand a better chance of getting a seat. Tell the taxi driver that you want a bus to Esteli and he will take you to the station. There are windows that sell tickets. Buy a ticket and wait where the bus will pull in. When the Nicas start lining up, you line up also. Have one person who is stowing the luggage below and another person who gets on the bus and gets the seats. Seating is competitive, extremely competitive. The buses that leave Managua can be jam packed with riders.
http://www.thebusschedule.com has good information about scheduling.