Cinque Terra to Lucerne - overnight journey

What date are you looking at? I cannot find this itinerary on the Flixbus website for October. The bus that arrives in Zurich at 3:40, is a connection that departs La Spezia at 17:55 with a 2 hour connection in Milan. I do see a direct bus that leaves La Spezia at 10 past midnight (12:10 am) and arrives Zurich at 8:10 am.

It is a lot of traveling to visit the Cinque Terre for half a day. There are five villages and you won’t have time to see them all. The transfer to Lucerne appears difficult and exhausting.

You will not get any closer bus departure point. La Spezia is the nearest town and next station to the Cinque Terre, and the only access to or between the 5 towns is rail or on foot.
"explore cinque terra for half day." - a day trip from where? It will be a very quick visit, hardly worth it. You are aware that Cinque Terre is an area of five towns, hence the name.

La Spezia to Zürich by overnight bus - I wouldn't do this. 6 hours on a bus overnight, no way I would sleep, then arriving at 03:40. I would need 2 days to recover.
There are no overnight trains from Italy to Switzerland. I would choose a day train, and go direct to Luzern (cut out the detour via Zürich). You are already planning to have a Swiss Pass valid on your day of arrival. A train from one of the Cinque Terre towns to the Swiss border, if bought today, only costs €18.40, but you are planning to pay €76 for an uncomfortable bus (times and tickets on http://www.trenitalia.com/tcom-en ).

When you ask "is it safe at this early in the morning in the bus station?", I guess you mean Zürich - yes, why wouldn't it be?
First train out of Zürich HB for Luzern in the morning is 05:35, you have a 2 hour wait (info from https://www.sbb.ch/en ).

I just looked on Flixbus for an arbitary date in October. I entered La Spezia to Luzern. It found one option:

17:55 La Spezia, Transfer in Milan (Lampugnano bus station) Arrives: 21:50 Departs: 02:00, Luzern 05:00, price £26.98

STILL NO WAY I WOULD TAKE AN OVERNIGHT BUS. This has 4 hours in a bus station in Milan in the middle of the night.
Why are you getting a bus to Zürich when there are buses to Luzern?
You have quoted a price of €76, But Flixbus says £26.98 a lot less. Flixbus is quoting in GBP because I selected English language. How did you get this price of €76?
Also, if you are planning to spend that day in Luzern, you save a day on your Swiss Pass.
BUT AGAIN, I WOULD NOT RECOMMEND THIS OVERNIGHT BUS

Hi there,

Thanks so much for the clarification. I was looking for overnight buses to avoid staying the night but looks like that is a much exhausting option. My bad, I think I maybe have mixed the ticket prices. From CT town - to which place do you recommend taking the train to in Swiss border? Also would my Swiss Travel Pass cover the journey for the next leg to Lucerne?

From CT town - to which place do you recommend taking the train to in Swiss border? Also would my Swiss Travel Pass cover the journey for the next leg to Lucerne?

Cinque Terre is five towns: Monterosso al Mare, Vernazza, Corniglia, Manarola, and Riomaggiore. There is a rail line along the coast linking them and each town has its own station. So start your train journey at whichever town you are in.
If you want to go to Luzern, then look up trains from whichever town to Luzern. You can do this on the SBB (Swiss Railways) website: https://www.sbb.ch/en
On this route the train crosses the border at Chiasso. A Swiss Pass is valid from Chiasso. You can see Chiasso on the Swiss Pass Validity map here: https://www.sbb.ch/content/dam/infrastruktur/trafimage/karten/karte-sts-pass-gueltigkeit.pdf
You then need to buy a ticket from whichever town to Chiasso. You can do this on the Italian Railways site: http://www.trenitalia.com/tcom-en This is where I got the €18.40 fare I quoted in my first post.

This ticket will be specific to a train and will include a seat number. If you already have your Swiss Pass you do not have to get off the train, just stay seated, it only stops at Chiasso for 3 minutes. When the Swiss ticket inspector comes round, show him/her your Swiss Pass. f you need to buy a Swiss Pass, you will need to get off the train at Chiasso, and catch a later train (1 hour later).

http://www.trenitalia.com/tcom-en

Sure thanks so much for the response, let me work it out!