I recommend staying at a hotel, close to the central station; Elite Adlon, Frey's Hotel or Scandic Klara, as Arlanda and surrounds are at the top of the list of europe's most uninspiring airports.
Stash luggage right away at one of the suggested hotels with 24-hour services. I did the same at Scandic Gamla Stan on Monday. They will gladly store it for you.
Walk Gamla Stan/Old Town. Enjoy unique Scandinavian treats such as Skansen (open air museum), the City Hall or the Vasa Museum.
Contemplate the beauty of soulful Scandinavian symbolist and impressionist paintings (1890-1910) at Thielska Galleriet (gallery/museum). Taste some lovely swedish fika (cinnamon buns and cookies with coffee or lemonade) at Vetekatten (café) or Grillska Huset (café). Have gelato, equal to that found in Italy, at Snö, or 45 varieties of ice-cream at nearby Stockholms Glasshus.
The best option for transport at that early hour would be the high-priced Arlanda Express (train).