If I may recommend a place to stay, we just stayed at the Park Inn by Radisson - Munich East. It is a 2 minute walk from the Johanneskirchen stop on the S8. It was a very nice hotel with a restaurant/bar and perfect for families. It is extremely easy to get to Marienplatz and other attractions from that hotel, and it would be quick to get back to the airport, as it's only a few stops down the line.