Berlin probably wins the über-cool style war but I suspect it will come down to which you can reach. Where are you starting from? No point in getting worked up about either until you're sure you can get there!

I can't comment on Munich but we spent last New Year in Berlin and would highly recommend it. There's a massive street party by the Brandenburg Gate with live bands, beer tents and food stalls etc... and a great atmosphere.

I am coming from Dublin, Ireland so getting there shouldnt be a problem? Leaning towards Berlin at the moment. Have heard a few good reports about New Years there.

Where is the best place to stay location wise? Mitte, Kreuzberg, Alexanderplatz, Scheunenviertel or where?

I think Mitte is the more central with plenty of bars, restaurants etc... but as long as you're near a public transport link you'll be fine. On New Years Eve the public transport runs all night.

Munich may not be as easy as you think, are you looking at the Ryanair flights to "Munich West"? This used be called Allgaü Airport and is at Memmingen which is quite a distance from Munich - in fact it would have been just as honest to call it Stuttgart South!! The direct express coach takes about 1½ hours and costs €36 return (slightly less if you book by internet). You can currently get there by ordinary public transport for €25 each way per group of up to 5 (price may change in early December) but that takes 2½ - 3½ hours.

So unless you've found some cheap Aer Lingus/Lufthansa deals to the real Munich airport things seem to be stacking up in favour of Berlin.