You don't need to arrange a Seine cruise in advance; just go when it seems right -- a nice balmy evening (take a warm jacket). There is one that launches under Pont Neuf Vedettes Pont Neuf. You can buy tickets on line ahead and save a couple of Euro and then use them when you feel like it (you exchange the voucher at the dock). They sell them for day and evening cruises. There is a dock with the larger flat boats near Pont d'Alma on the right bank and near the Eiffel Tower on the left. If the boat is full when you arrive, there will be another one along shortly. Just not something you need to arrange ahead.
The Museum Pass is a convenience for the first trip; you can skip the long security line at the Orsay and use a special door with a short or non-existent security line. You can use a shorter security line at the Pyramid for the Louvre. There is a separate line at the Orangerie. At Versailles you have the super long security line and there is just one; just arrive about half an hour before the chateau opens and you won't have too long a wait and you can skip the ticket line once inside. With the museum pass you can also make brief museum stops without having to think about costs.
If you don't go with the pass then you can book timed Louvre tickets on line. I have been to the Louvre a couple of dozen times and never had a long wait because I used entrances other than the Pyramid, but I think there are fewer entrances and more security concerns now and so having the pass is not a bad idea -- or a timed ticket.
The one ticket you need in advance is the Eiffel tower and those go up and are sold out quickly 90 days in advance.
