I'd probably say Stockholm, because there's arguably more to do and because it's a more interesting backdrop IMHO.
If you do go for Stockholm I would thoroughly recommend Hotel Skeppsholmen, which is on the museum island, in a quiet and leafy location but only a short walk from the centre. The rooms are fabulous (yes, I said fabulous) and the breakfast is fucking incredible. It's a so-called 'design' hotel, so every last detail is immaculate.
Also, you'd HAVE to eat at Bakfickan ("Back pocket"), a tiny brasserie at the opera house. Great atmosphere, ludicrously delicious Swedish meatballs and not that expensive.
I'd also recommend a trip around the archipelago as well as a cycle around some of the islands near to the centre. Beaut.
One last tip. If you're stuck for something to do at any point, catch a film at the Skandia cinema (Drottninggatan 82). The interior was designed by Swedish architect Gunnar Asplund and is proper beautiful.
There you have it folks. Thread ends.