If you find long lines at the Eiffel Tower, consider a stroll to the Tour Montparnasse. Shorter (or no) lines and a much less crowded viewing area. Not as high up, but the view includes the Eiffel (and excludes the unattractive tower you're on top of). The nearby cemetery is also interesting and historic, and there's a good street market on the Rue Daguerre.
The ET is of course visible from everywhere, and well worth approaching to get a sense of its size and appreciate its geometric beauty. (Also FYI a center for pickpockets, but don't let that deter you.) I went to the top and it was fine, but a lot more work than for comparable views elsewhere.
If you can handle the stairs to the top of the Arc de Triomphe, there's a fine view there as well. And also from the towers of Notre Dame, including the gargoyles and gothic tracery right next to you -- but the towers are where you may find a long line, and the stairs are medieval and difficult (is that an oxymoron?). If time allows at ND, try to get down to the archeological crypt under the terrace (parvis) in front of the cathedral.
My estimates for your sites: Notre Dame one hour (inside and out) unless you line up for the towers. St-Chappelle one hour plus whatever waiting time in line (it's a security line for the court buildings around the chapel, not the chapel itself). Eiffel Tower who knows? Arc de Triomphe half and hour, or maybe longer if you go to the top. Champs Elysees half an hour plus any stops. Marmottan one hour or more, depending on your interest in Monet and other artists. It's also a little ways off from the Metro, but through a pretty park. Montmartre a couple of hours, including Sacre Coeur, the view, Place du Tertre (more pickpockets) and work your way down the streets.
