Any recommendations?
"Nice hotel" is such a relative concept - are we talking 1-star hovel, or 5-star palace, or somewhere in between? Which side of the Bosphorus? Etc. Much better if you look yourself on one of the booking sites like hotels.com or booking.com, that way you may be able to pick up a nice bargain.
But if you want personal recommendations, then I like the Sofa Hotel in Ni?anta??, both for the hotel itself and for the location, and the restaurant on the roof.
Sufi Hotel Apartments are good, and affordable.
As Orakle said, you need to specify what you want. If you just mean a clean, roomy, quiet hotel, there are loads of them, and many don't cost much (e.g. $40 or less).
The Marmara is one of the best hotels if you can afford.
http://www.hilton.com.tr/
if you can afford.