I highly recommend Ra’s apartment its clean with beautiful views of the Bosphorous. The location of the apartment is just perfect very close to Taksim Square , Galata Port, the palace and it has good links to the tram. We actually walked from the apartment to the blue mosque it was a bit of a long walk but we got there in less than an hour with young kids :)
The host is very responsive and helpful I got some nice restaurant recommendations. In short this apartment is a fantastic place to stay to explore Istanbul.