The scenery along the thruway is not spectacular in my opinion. It does have its pleasant areas, but that's about all. Maybe going to and from college in Rochester has simply jaded me to the thruway through overuse.
I-86 to I-88 is just as pretty, and not toll. As I recall, I-86 had some very rough sections in the western bits, but I think most or all of them have been repaired in the past few years...though I don't know for sure. Some here also think I-88 is terrible, but that has not been my own experience with it...it's not glassy-smooth, to be sure, but neither has it induced a headache or loosened fillings or caused the dishes to be dispersed randomly throughout their cabinet in my RV.
Taking secondary roads along the lake shore, St Lawrence, or through the Adirondacks would be more scenic in my opinion, if possibly a little slower going. If speed is your main concern, the Thruway it pretty much must be.