In winter the air is clearer (less humidity in the air) so that you are likely to get to see Mt. Fuji better, even from Tokyo, though of course quite from far :) But it also depends on the weather so noone can say anything for sure. I don't know what kind of bus tour it is, but if you are interested in natural scenery I'd say why not :) Try searching the internet for Fuji Hakone tour - there are some travel blogs that list short movies taken during such bus tours.
If you have some time, though, you can plan something like a 2-day trip to Hakone on your own (from Tokyo), viewing Mt. Fuji from Hakone (from Lake Ashi, etc.) and enjoying a stay at a hot spring inn. Just a thought.
