Radio City Apartments on West 49th Street comes highly recommended.
We stayed in a 2 bed apartment for 3 nights in July and cannot praise it highly enough - excellent tripadvisor reports - round the corner from Times Square but not too close either! and just up the road from the Rockafeller Centre with all the sub stops very close and handy. Oh and one last thing, theres a cafe called Toasties just outside the door that do breakfast wraps to die for!
we stayed at the Radio City Apartments too a few years back
great location, clean and basic
we also stayed in the shearton off times square ,
we are staying in the hillton this time
most hotels in NY are small rooms with 2 double beds not super kings size like you get in Orlando