Lodging in Varenna is tough. I couldn't find anything suitable for me at a reasonable price for this year's trip. I ended up in Tremezzo at a comparatively affordable place within walking distance of a ferry stop that was served fairly often, as well as not too far from a bus stop. However, being right in Varenna, Bellagio (probably more expensive) or Menaggio would really be more convenient; I think they're served by more frequent ferries. Varenna also has great train access, and the other two have a lot more lodging and restaurant options. There are some sightseeing pluses to being on the west side of the lake (which Bellagio is not, but Menaggio is): proximity to Villa Carlotta, Villa Balbianello, and the Lake Como Greenway. I quite liked Menaggio, though it isn't quite as cute as Bellagio or Varenna.
For most of us, finances place some limits on our lodging choices. For a long stay like yours on Lake Como, I'd pay a lot of attention to the convenience of the location, but then I'm not one who falls in love with a hotel because of the decor or the view, and I'm not interested in relaxing around a pool, however beautiful the surroundings. Then again, it can be very hot on Lake Como in mid-summer, so a pool would be appreciated by many people.