Not the cheapest time for Berlin.
You could go for Econtel (***), which is available for 47,90 (between the airport and city west and a X9 bus stop for Bahnhof Zoo and the airport in front of the hotel). You could go for A&O Hauptbahnhof (**), close to the central station and well linked to both, City East and West for 59,00. Grand City Hotel Berlin Zentrum (***) in the very heart of City West (good location, perfetly linked to all kinds of public transport) offers a 3-4-2 and a total of 178,00 for the three nights (close to Ku-Damm).
Several of the cheap locations are in the suburbs. These three are the most central and bearable ones I found.