I took the Vedettes du Pont Neuf tour, there are seats outside on the front of the boat. There are several different boats, all have some outside seating and I think even if inside, the scenic side windows open. At lease one boat has an upper open deck and at least one doesn't.
Buy the tickets on-line and save considerably! When you get there, there is a special window for vouchers.
When I took the tour, sunset was around 9.45 (June), I took the 10 pm boat. I arrived just as they started boarding at 9.30 and got a front seat. It was about 10.15 when we got to the Eiffel Tower. I found this to be an ideal time with about half the one-hour tour at dusk.