We have six days post river cruise to spend in this region. Our thought was a train to Lyon for three nights, then to Lucerne for three nights. Have tried to search for travel options (swiss pass/euro pass/direct purchase train tickets) but finding it very difficult especially when trying to figure out what side travel is included for Lucerne. Could anyone comment? Also, would love your recommendations on what to do in Lyon and Lucerne.
Thanks.

For info on train travel in Europe, including info on passes, go here: https://www.seat61.com/

If you are in Lyon, why not go to Annecy and Chamonix rather than Lucerne?

It will take a whole day to train between Lyon and Lucerne - leaving your 5 days. And Basel to Lyon would take about half a day. 4.5 days.

I'd suggest concentrating on Lucerne and another place closer to Basel - like if you have not been to Switzerland's awesome high Alps the Jungfrau Region around Interlaken - just a few-hour train ride from Lucerne and Basel. Ensonce yourselves in a cute mountain village like Wengen or Grindelwald and take a myriad of thrilling aerial gondolas and mountain trains going off in all directions - hiking paths for all degrees of difficulty - the Switzerland etched in most peoples' minds but which Lucerne and Basel, nice as they are, will not fulfill. Annecy and Chamonix suggested by thrusdayds would be sweet too - The French Alps at Chamonix being awesome too and Annecy a lovely city on a lovely lake.

Unless you stay in Switzerland and visit two places - like Lucerne and Jungfrau Region forget about any passes - but if 6 days traveling from bases then a Swiss Pass could be a great deal or a Half-Fare Card (see www.sbb.ch for details) - for lots on Swiss trains and French too check www.seat61.com - great info on booking your own online discounted tickets say if going to Lyon; general train info like where to go by them check www.ricksteves.com and BETS-European Rail Experts.

Why do you want to go to Lyon, if you don't know what to do there?
Discounted web fares for the direct Basel - Lyon train start at 30 EUR, standard fare 70 - 100 EUR, according to the itinerary.
Have a look at the site of French railways
https://ch.oui.sncf/en/
Standard fare for a Lyon - Lucerne ticket (via Zofingen, not along the scenic itinerary): 100 EUR

Train journey times:
Basel - Lyon (direct train): 3 1/2 hrs
Basel - Lyon with change at Mulhouse or Dijon): 4 - 4 1/2 hrs
Lyon - Mulhouse - Basel - Lucerne: 5 - 5 1/2 hrs
Lyon - Geneva - Zofingen - Lucerne: 5 - 5 1/2 hrs

Thank you for all for commenting and for weblinks and information. I'm sorry I was unclear. My concern was what was included with the train pass when visiting the Lucerne area. I will go to the website suggested and see if there is a better list than what I was finding. I think we have, however, made the decision not to rent a car and drive. We will also look at the other locations suggested so that we can finalize our plans.

Look up the valididty map for Swiss Passes as this has exactly what is covered and what is covered in full. www.sbb.ch. With six days in Switzerland a Swiss Pass probably would be a good deal unless sitting in one location and not doing much.

https://www.sbb.ch/en/leisure-holida...avel-pass.html

And things covered do change - like I guess Pilatus was 100% covered first time last few years but too many Swiss Passes used it so now it may be back to 50%? Not sure but the point is consult a 2018 validity map.

Basel - Lyon trains are operated by OUI (SNCF). For Lyon - Lucerne, you have the choice between the itinerairy via Basel (most of it operated by OUI) and that via Geneva (most of it operated by SBB).
The OP may also use the flixbus between Lyon and Berne (6 hrs, 15 EUR/pax)
or the Swiss Express Bus between Geneva and Lucerne (with bus change at Rothrist)
Therefore I think that a Swiss Travel Pass might not be of any help.

We traveled from Basel to Lyon the day after Christmas in 2016. It was an easy taxi ride to the train station from the disembarkation point of the boat. We spent a lovely three nights in Lyon before heading to Paris for New Year's. The food, of course, is the attraction in Lyon, and it is an interesting small town as well. You can book a free walking tour with Lyon City Greeters (Lyon City Greeters ? english | Un site utilisant Réseau Lyon City Greeter), which is organized by the tourist bureau there. We also enjoyed the hop on, hop off bus tour around the city and were able to get an overview as well as some very nice photos.

We went to lunch at Restaurant Vattel (Restaurant et salons Vatel a? Lyon Perrache en France - Restaurants Vatel), which is part of a renowned culinary school. Lunch was fabulous, and I have heard that dinner is as well.

Swiis Travel Pass valid on Swiss Lucerne-Geneva bus neckervd? Just curious not that OP needs a Swiss Travel Pass.

Perfect - just what I was looking for. Thanks!

TO PALEN:
Yes, but that wouldnt't make any sense, as the trains are direct, faster, more comfortable and they run every hr.
The bus might only be a solution for people with no travel pass ho want to economize a few francs.

Again neckervd thanks and since I never heard of those I think relatively new long-distance buses I appreciate the info in my stride to keep up on all things Swiss travel!

If I found myself in Basel, that is that same as Mulhouse, and I would visit Alsace instead and save a bundle over those Swiss prices, where you will spend 3 times more. I am a skinflint.

You can travel Switzerland on a low budget as I always have -but you have to know to go to certain areas which thankfully are Alpine splendors like the Interlaken-Jungfrau region where inexpensive hotels, pensions, B&Bs and things like the Nature Friend's House and hostels can keep costs low. Supermarkets have take-out deli food and of course everything you'd expect and prices are higher but not nearly 3 x. A Swiss Travel Pass can keep transport prices very low. Now restaurants and cafes and 'good hotels' are much more expensive those but these costs can easily be avoided. I usually spend about the same in Switzerland as I would in other countries - but have to forego things I would eat and do in other countries - so it can be done so don't be deterred by the often overbloated hyperboles of how awfully expensive will be - it easily could be but don't have to be.

SWISS INTERCITY BUSES
Yes it's brand new. The first buses will run in 3 weeks, on 4 lines:
Zurich - Baden - Basel
Basel airport - Basel - Olten - ROTHRIST - Lucerne - Stans - Fluelen boats'pier - Bellinzona - Lugano
Sion - Martigny - Montreux - Vevey - Bulle (Gruyeres) - Berne - ROTHRIST - Zurich - Chur
Geneva - Lausanne - Yverdon - Neuchatel - ROTHRIST - Zurich - airport - St. Gallen

And Swiss Passes valid on all, right?

What's the reason for those buses? Quicker than trains? Cheaper of course but if lot longer...