Hi, That's cutting it kind of close. La Costeña expects you to be there for check-in 1 1/2 hours in advance, and if the flight is sold out, they start giving up seats for standby passengers.
However, they do keep track of arriving Intl flights, and I'd suggest giving them a call to let them know when you'll be arriving, and see what they can do.
You're right BTW, it will take a little time to get thru immigration and customs, depending on if other flights are also arriving when yours does. Once you're out, go left when leaving the Intl terminal.. La Costena is at the other end from the exit where you come out of customs.
If you get stuck overnight, there's a Best Western across the street, and a great place called Camino Real a short shuttle ride away. I also highly recommend Managua Hills B&B.. About a $15 cab ride away, but much cheaper than the airport hotels.
Hope you make it, and make sure to visit Little Corn while you in the area.. It's a "don't miss".
Hope this helps!
J