The options on the Gotthard route are:
Use the new base tunnel (the longest tunnel in the world), the Intercity trains run Arth Goldau - Bellinzona non stop *
Use the old mountain route on ordinary regional trains - for this you take a train from Zurich or Luzern to Erstfeld, or a boat from Luzern to Fluelen then a train Fluelen - Erstfeld, then the regional train Erstfeld - Göschenen - old tunnel - Airolo - Bellinzona - Lugano - Milano
Use the Gotthard Panorama Express(GPE): any train or boat to Fleulen then the GPE. Personally ** I don't think it is worth the extra expense, as the regional trains have large windows
It is a myth that the Gotthard Base Tunnel (GBT) 'removes' all the scenery from a north - south train ride over the Gotthard route. Between Zurich / Basel / Luzern (the three main city northern origin points of Gotthard journeys) and the GBT tunnel entrance near Erstfeld, you get plenty of mountain and lake views and an awful lot of classic Swiss rural farmland scenery, and the same applies when you exit the tunnel at the south end near Biasca.
** Gotthard Panorama Express - a personal view
This is ‘take it or leave it’ advice:
Personally I am sceptical of the attraction of the Gotthard Panorama Express. It is an attempt to keep some tourism going on the Gotthard 'mountain route' since the rest of the fast trains now go through the base tunnel. However, you see mainly valleys not high mountains. Also it is reservation obligatory and first class only.
Also, the train gets rather lonely - part of the ‘romance’ of the Gotthard route previously was that your train competed for space on the line with huge long international long-distance trains carrying 000s of passengers a day between northern and southern Europe, and those passenger trains interacted and weaved in between dozens of heavy freight trains lumbering back and forth across the Alps.
The curiosity was seeing another train high above you one minute then a few minutes later passing by your train on the same level, then perhaps seeing it again below you a few minutes after that. It is this that no longer happens as there are so few trains left on the line.
(It could also be argued that it is just a way of finding a use for very expensive panorama cars that Swiss Federal Railways bought but don't have now have any other use for them...)!
More economical might be for you to take any boat Luzern - Fluelen. Then take the train Fluelen - Erstfeld. Change at Erstfeld into the regional train that takes the same old mountain route but at no extra cost, and runs direct through to Como (and Milano)