My flight in May was delayed so I had lots of time at the San Juan airport and I checked out the hotel's public areas. It was pretty plain and basic, but the public washrooms were clean. If you are planning on heading straight to the port it would be ok.
Before our cruise we stayed at the Hampton Inn Isla Verde and it was very nice. My sisters flight arrived at 1:00am and she had no issues taking a taxi to the hotel , it is only 5 minutes away and cost about $10.00. The morning before the cruise we were able to go to the beach for an hour or so, it is about a 5 minute walk from the hotel, so to me that is an advantage over staying at the airport hotel.
I always like to have something to do the morning of a cruise as time seems to go so slow if we are sitting around in the hotel waiting to go to the port.