Suggestions for a 3 day base in early April arnd Zurich

Of the list you gave, really love Stein am Rhein. Very quaint and beautiful. Not much to see once you've walked around and done the Abbey (a must), but we loved going up and down the Rhine, which could fill out other days. It would be very laid back and unrushed.

Between Bern and Basel, I'd definitely give the nod to Bern. Basel is nice, but Bern has more charm.

One not on your list that I think might fit the bill is Neuchatel. About 90 minutes west of Zurich, it gives you access to the Three Lakes region for castles, wine, nature walks, and beautiful settings. Definitely NOT the classic Swiss Alps, but quite picturesque and good for your time of year.

Hoping to see beautiful landscapes, the famous cows & the scenery!

Of your list, I would say that Zug, and even more so Appenzell would fit this description. I haven't been to Einsiedeln, but photos of it look pretty beautiful!

I don't know it it interests you but there is the Cherry Blossom trail in Frick in bloom in April

https://swissfamilyfun.com/cherry-tree-trail-in-frick/

Get a 3 day Swiss Travel Pass (it gives you a lot of mountain top and lake excursions and covers all museums in case it rains) and stay in Bern or Luzern and take day trips from there. Bern is quieter than Luzern. I'd avoid basing in the towns that you mention like Appenzell.

Thank you all for your feedback & for giving so many options to consider. I am still confused on where to base myself for 2-3 nights (other than Zurich) or would you still recommend basing in Zurich & doing trips from there? Ideally I do want to spend some time away from Zurich but also a place I can connect to & from easily for trips depending on the weather.

I do like Luzern, 45 minutes by train from Zurich HB. Many scenic boat rides and mountaintop rail or cable car trips. Train to Engelberg and Mt Titlis. Train to Meiringen over the Bruenig Pass, Reichenbach Falls and Sherlock Holmes Museum, lots of cows along the way if they are out of the barns.

Any recs on specific villages to stay in on Lake Thun or Lake Brienz that may are well connected with public transport. Really trying to look for a small-ish town/ village whilst keeping other options open as well.

Have you looked at this map of the Swiss transit system? It might help you answer some of your questions (blow it up until it is big enough to read). For example, you can see that Spiez has a number of rail routes (the red lines) radiating out in several directions. Thun has some rail, but has a good concentration of bus routes (yellow). Play around with it and see if you can spot an obvious transit hub that also fits the bill on what you'd like landscape- and scenery-wise.

Thanks @History Traveler- this map is very helpful. I hadn't seen it before. On it now!