I would not bother with the excursions. I usually like bus tours but the traffic in Paris makes them slow and hard to see much in a day. The trains are much more efficient.
The main train station is right at the entrance to DLP and you can catch the RER Red line into the city in about 45 minutes. Notre Dame, Saint Chappelle, the Louvre, Musee D'Orsay are all within a few minutes walk of each other. You will need to get back on the train to go to the Eiffel area (just 5-10 minutes by train). I would recommend Rick Steve's downloadable walking tours as they are free and great guides for most of the sites. Also, a guided tour of the Eiffel makes going up easier (lines are typically long) - I used CityWalks and did the Eiffel and Night Cruise of the Seine and that was excellent. Be careful to leave Paris to be back by around the time DLP closes unless you are staying within walking distance as the taxis will not be available.