I'm just back from another 4 days in Paris, and here's where I stand on this. The tower should be booked ASAP, as should the Musee d'Orsay. You want to do this because you want specific times. You want the first opening time at the museum. You want 30 minutes (minimum) before sundown on the tower. The catacombs don't matter because they're underground.
I highly recommend both the Petit Palace, open now after a couple years restoration, and the often overlooked Musée Marmottan Monet if you have any interest in Impressionist paintings. (The current, temporary, exhibit of works by Eugène Boudin is very good).
If you want a souvenir you'll actually use go visit Laguiole en Aubrac, one of the very few local, traditional, knife shops and pick up a kitchen knife or two. Or a pocket knife if so inclined. Fantastic work, reasonable prices.
There is a day pass available on the metro. But you'll pay 20 euro a day for that. And odds are you won't need that many trips (average cost is 2.50 euro). If you can avoid the line at the Gare d'Est where all the tourists jam up to the very few machines (I've done this too). Go to one of the smaller metro stations and there the machines will not be crowded. You can easily be 30+ minutes in line at Gare d'Est. Take a cab to your hotel or walk to the next stop (they're not that far).
There is a hop on - hop off boat (no ferry) but I've never seen a reason for that.
Also, if you're anywhere near a French Bastards bakery, stop in. Likewise Plan Chocolate on the Rue du Nil.
Bistro Vivian in the Gallery of the same name is very good. And I had several old friends who made up a party at La Florintine and we had a great time.
The Ferris wheel in the Tuileries is worth a ride after the sun goes down.