Across not through the Alps

The only train that goes "over" the Alps is the Berinina Express. That would require getting to Tirano first.

All other routes go through tunnels. What you can do is take the old line over the Gotthard, which involves a shorter tunnel. In order to get the schedule for those on www.sbb.ch just enter "Göschenen" as a via.
SBB can sell you a ticket all the way form Florence to Luzern.
(Do you have your ticket already?)

Thankyou. That was the answer I was looking for.

Do you have your ticket already?

Note: If you are not in a hurry you could take one of the regional trains from Milano to Locarno, spend a few hours there, and then take one of the direct Locarno - Luzern trains that go over the old mountain route.

It is unlikely that from Florence you would get to Tirano in time for the morning named train Bernina Express. There is an hourly local train which goes the same route, stopping at the same stations - or more - with a change or two on the way to Chur from whence you can get a train to Luzern.

Whichever way you go on that very scenic route you should devote the whole day to moving north. It will be fast train to Milano Centrale from Florence, then change to the hourly TreNord train to Tirano which takes about 90 minutes. Then the several hours on the Bernina route, then the train from Chur to Luzern with one or two changes.

If you go to the route via Andermatt you will have the old route to Luzern from Milan, slow and scenic, but considerably faster than the Bernina.

You already know that the trains tunnelling under the Alps are way faster and much less complicated.

Is your question because of an aversion to tunnels - several people here have that issue - or for the most scenery on the way?

The rail line between Milan and Tirano is still blocked by a landslide. Replacement boat service is the work around, so it will take longer.
https://www.trenord.it/en/

The Treno Gottardo is a scenic route that goes mostly over the Alps via the Gotthard Pass ( there is a short tunnel at the top, but still lots of scenery on the way). You start in Locarno and it goes directly to Luzern with not changes, taking 3 hours. There are trains departing Locarno at 11:35, 13:35, etc. This may be a more realistic option than the Bernina Pass route with bus substitute for the blocked section.

https://www.myswitzerland.com/en-us/experiences/treno-gottardo/