I'd stay at the City Hilton. Monday morning check out and leave the bags at the Hilton buy a Single person Tageskarte Gesamtnetz for €10.80 from the machine at Rosenheimerplatz S-Bahn go to Marienplatz have a quick beer in the Hofbrauhaus(yes it's touristy but so what if you've never been to Munich) then go to the Viktualienmarkt and sit in the small biergarten there(one of the few that you can guarantee is open as long as it isn't absolutely lashing down rain) and get some great food from the stalls and watch the world go by. Perhaps even climb the tower of Old Peter for a great view. Then go back to the Hilton for about 1:00 P.M. grab your bags and get back on the S-8 to the airport for your 4:00 flight. I've done this so many times with friends and solo it's a great routine for our last day in Munchen.

If you have more than a beer make sure you go to the toilet at the Hilton before going to the airport as it's about 40 minutes on the toiletless S-Bahn.