Hi romil, and welcome to MySwissAlps!
In my opinion, neither option is central enough to be convenient, due to excessive travel times to the places you plan to visit.
Lungern to the Jungfraujoch - 3 hours 13 minutes one way
Lungern to Titlis - 2 hours 22 minutes one way
Lungern to Luzern - 50 minutes one way, hourly service
Lungern to Glacier 3000 - 4 hours 48 minutes one way
Lungern to Zermatt (for Glacier Express) - 3 hours 22 minutes one way
Lungern to Broc-Fabrique (chocolate factory) - 3 hours 19 minutes one way
Niederreid to the Jungfraujoch - 2 hours 20 minutes one way
Niederreid to Titlis - 3 hours 48 minutes one way
Niederreid to Luzern - 2 hours 16 minutes one way
Niederreid to Glacier 3000 - 3 hours 25 minutes one way
Niederreid to Zermatt (for Glacier Express) - 2.5 to 3 hours one way
Niederreid to Broc-Fabrique (chocolate factory) - 3 hours 09 minutes one way
This is what I would suggest:
For Luzern/Lucerne and Titlis - somewhere central in Luzern
For the Jungfrau - Interlaken, Wengen, Grindelwald or Lauterbrunnen
For the chocolate factory - Montreux
For Glacier 3000 - it's quite out of the way, so not sure. Maybe Sarnen or Gstaad. Perhaps someone else has a better suggestion.
For the Glacier Express - to do the whole route, which takes about 8 hours, you really need to stay one night in both Zermatt and St Moritz. For information on doing part of the route, see the heading Don't have time to do the full route? on this page:
Using the Swiss Timetable will assist you with travel times and routes between wherever you decide to stay, and the places you plan to visit.