I like Menaggio. It’s very quaint also and has lots of restaurants and hotel choices as it’s a bit bigger than both Bellagio and especially Varenna. Every night in summer they have live classical music on Piazza Garibaldi, the main plaza on the lake where most sidewalk restaurants and cafes are (the area is entirely pedestrianized). There are lots of choices of good restaurants in Menaggio, even just in the same plaza. You can’t possibly try them all unless you stay a long time. Bellagio may have a bit more since it’s the most popular tourist town, but not much more. Varenna is much smaller than the other two so obviously can’t have the same number of choices as Bellagio.
Both Varenna and Bellagio are across the lake. The passenger ferry coming from the north (Colico) in nearly all cases, stops first in Varenna, then goes across to Menaggio, then from Menaggio goes to Bellagio and so on all the way to Como. The one coming from the south (Como) does the reverse, stops in Bellagio then Menaggio then Varenna. The crossing time from Menaggio to Bellagio is 8 min, from Varenna to Menaggio is 5 min. therefore you can very easily stay in Menaggio and take day trips to the other two, as ferries are frequent.
As I said I generally had dinner in Menaggio (or in any case on the same side of the lake), because I enjoyed the classical concerts while dining at the many restaurants on the plaza. I only had lunches at Bellagio and Varenna when I was in Menaggio (although I’ve also stayed in Bellagio in years past). If you have dinner in some of the other towns across the lake (like Bellagio or Varenna) and stay late, you will need to rely on the taxi boats to return to Menaggio, which are rather expensive unless you are in a big group. That is true no matter what town you choose. Dinner will have to be on the same side of the lake where you sleep because You can’t really go back across by ferry late at night.
I also enjoyed Menaggio because it’s a quick drive to Lugano (Switzerland) and my wife loves the place (if not the prices). By car (I had a car) you can be in downtown Lugano in 45 min or less from Menaggio. If you don’t have a car there is a bus that goes back and forth, I imagine in about one hour. I don’t know how late it runs but probably not late enough to have dinner in Lugano and make it back by night. But you can certainly visit Lugano during the day by bus.
Not sure about hiking trails. But nearby you can visit Villa Carlotta (in Tremezzo) and also the spot where Mussolini was captured and killed by the partisans before his body was displayed upside down in Milan (Villa Maria in Giulino di Mezzegra).
EDIT: below is the Menaggio - Lugano bus schedule.
http://www.menaggio.com/ita/e-lakes/Orari_bus.pdf