It's pretty easy to avoid the bad parts of Managua. Yes, parts can be dangerous, like any large city, including San Jose.
We used Paxeos to get from Granada to SJdS, and they did a fine job. For a night drive between MGA and Granada, my first choice would be an unmarked private vehicle. Just to avoid getting targeted as a tourist. But I would be willing to do the trip in a taxi or tourist van too.
If you are too concerned about the night drive, you could always just stay at the Best Western right across the street from the airport. They'll even come pick you up so you don't have to walk across the street.