Really? You can't just go and see highlights of the Louvre in one whole day? That worries me as I was planning on spending one day in Paris for two museums. I don't need to see every exhibit, though.
Depends on what you consider highlights, there are plenty of tourists who go into the Louvre, walk straight to the Mona Lisa, snap a picture and then leave.
On a crowded day, those tourists look like this.
Browse through the catalogue and determine what you would find interesting. Then determine how much time you need.
What is the other museum? D'Orsay?
With the tour you only get 1.5 hours in the Louvre if I understand correctly.
I would just go on your own, not just because it might be cheaper, but to also roam around at your own pace, leave whenever you want...
Don't worry about getting to Paris, if You can navigate through a big city or even an airport, you will be fine. Get yourself a subway map and go!
One tip: if you get the subway ticket from the machine, don't put it next to your bank/credit cards in your wallet. I had several times that the magnetic strip on the paper ticket got deactivated. If that happens, just follow another traveler through the gates, or try to find a subway employee.
Subway to Paris roundtrip €15
Access Louvre €17
Top of the Eiffel tower €25
River cruise, starts online from €10, but depending how long, with commentary there is a lot of variety.
If I had to pick a view, I would either climb the hill to the Sacre Coeur or my personal favorite: go up the Notre Dame.
The view is great and it has a Disney connection