Jungfrau

You can only go by bus to Lauterbrunnen then the rest has to be by train. The train from Zurich to Lauterbrunnen is easy and relatively fast, especially if you go through Bern. The trains in Switzerland as a whole are wonderful.
Definitely do the trip by train.

As mentioned above, the bus doesn't go to the Jungfrau. The farthest you can go is Lauterbrunnen. Then, the journey up and back is not fast. It takes 2hrs to go up and 2hrs to come back down. The train that takes you there has a 3rd rail in the middle that is engaged by a wheeled cog. It does great going up and down. You will change trains at Kleine Scheidegg. You can easy do this yourself. At the train station in Zurich, you can buy a round trip to the Jungfraujoch. The Jungfraujoch is Europe's highest train station. Be aware that the ordinary round trip fare from Lauterbrunnen to the Jungfraujoch is about $180. Expect a roundtrip train fare of about $152. Total round trip is estimated at 324CHF ($332). I see this fare on the Swiss rail website (www.rail.ch). I'm curious as to the cost of the bus tour.

The bus tour is $235 for an 11 hr. trip. It doesn't post any info regarding how much time we'll be allowed at the top or at any stops, so we think we might prefer to make our own schedule. But are there long periods inside tunnels on the train? We'd be missing scenery!
Our daughter has been living in Zurich for a few months and can figure out the trains for us, so no problem in that respect. Thank you so much for your quick replies!

From Zurich to Kleine Scheidegg won't be too bad as far as tunnels go, and I wouldn't worry about missing scenery, you'll get lots of awesome scenery on the train in Switzerland, trust me...lol. As for the train from Kleine Scheidegg to Jungfrau, a good portion of that trip is in a tunnel, after all, the train is climbing a mountain, and the route is carved into the mountain itself. But no worries, the views at the top are great! For that matter, even going as far as Kleine Scheidegg and stopping there you'll be treated to some spectacular Swiss alpine scenery.

That's a really good price for the trip. As a group, I would assume that they have a reservation on the second train at Kleine Scheidegg. This really helps. Also, the train from Kleine Scheidegg to the Jungfraujoch does go through tunnels. In fact, the Swiss bored a hole right through the Eiger. The train does stop at a couple of viewing locations in the tunnels where you can look out windows. The Jungfraujoch is inside the Jungfrau. But, once you go up into the buildings, the views are breathtaking.

If by bus you mean an organised tour on a specific day then no never. Because if the weather is bad you will have wasted your money, and going from Zurich even if the weather there is good it may well not be at Jungfraujoch. Zurich to Interlaken Ost, the start of the Jungfrau trip is over two hours by train, the journey from Interlaken Ost to Jungfraujoch is another two hours. That for a return trip is eight hours in a train. The longest tunnel on the route is between Kleine Schidegg and Jungfraujoch, approx 50 minutes with two short stops at the viewing points in the tunnel. If you go make it a round trip and go one way vis Wengen and return via Grindelwald, starting and fimishing at Interlaken Ost station. If have any fears of claustrophobia then the short tunnels between Lauterbrunnen and Wengen may help you make your mind up. When you change trains at Kleine Scheidegg just take the train straight down to Grindelwald running at the bottom of the north wall of the Eiger. I hope this helps, it is a wonderful trip and well worth go on.

Yes, thank you for all the details, it does help!

What does the train from Lauterbrunnen cost and isn't there a pass that save you money?