Use the forum search for hotels, there's been several mentioned - personally, I'd go for the Sirkeci area as it's close to the ferry terminal at Emininou and an easy walk to the Grand Bazaar, Egyptian Market, Topkapi, Blue Mosque, Hagia Sophia etc. Its also got a tram stop for when venturing over to Besiktas, Taksim (change at Kabatas for the Taksim funicular) Ortakoy etc.
Ataturk is the most straightforward for getting into town. As Colwyn says, metro to Zeytinburnu and then you're on the tram line which has a couple of stops that make it easy to get to the hotels in the Sirkeci area.
Get an Istanbulkart which is valid for all public transport - you can get one at Ataturk Metro station and use it travelling in to town. Makes it easier than buying jetons and works out cheaper as well.
JF