Each has their pros and cons.  In call apartment are probably a less expensive alternative, depending upon the length of the session, although not necessarily.  I am assuming here that by apartment you mean a rent-able in call location.   In my years I have seen some well appointed incalls and less so.   But IMHO the quality of the company always trumps the location.

 Hotels, of course, can vary depending upon the season, and I gather the most efficient way of booking a room is last minute on priceline or similar sites, which creates a mixed bag of locations.  

   All the above notwithstanding, as a New York located client, I confess that I enjoy hotel sessions as it is the only opportunity I have to experience hotels in New York, since I never have the opportunity of booking a room for my own use.  One of the nice things about the hobby is that I have had the opportunity to experience some of the cooler hotels which I otherwise would never have enjoyed.   One fun opportunity is, once summer returns, to book a session in a hotel with an outdoor pool, of which there are a few.  Nothing like playing hooky from work, having a wonderful interlude, and then spending an hour or so basking by a pool with drinks.