If you go via Andermatt, you will be backtracking on the Glacier Express route. You can still turn this into a great scenic trip if you then go from Andermatt to Göschenen, then Flüelen, then on a boat to Luzern.
The train journey to Flüelen takes about 3:15, and the boat trip (hourly) takes 3 hrs.
Or you could go via Brig, the old Lotschberg railway to Spiez, then to Interlaken Ost, and the Luzern-Interlaken Express to Luzern. Total travel time is 5:30. To find this route, specify "via Kandersteg" (to force routing through the old Lötschberg Railway instead of the base tunnel) and "via Meiringen" (for the Luzern-Interlaken Express instead of the quicker route via Bern).
Given the choice, I'd go through Andermatt, because the boat trip is more "unique", but it is hard to choose!