On my very first trip to NYC a few years back, I did the Gray Line tour along with the full (3 hour) Circle Line boat tour (there was a combination price). I found the boat trip to be more interesting. If you only have time to do one, do the boat tour. The Gray Line bus is hop on/off so it is nice if you decide you want to get out and see something along the way. The bus is a good orientation to the city.