Both are beautiful, clear lakes. Charlevoix is larger and a bit more difficult to navigate, but also a bit more to see, so it may depend on how experienced of a boater you are & much work you feel like putting in. If you are on Walloon, Barrel Back is a fun spot for lunch or a drink; if you are on Charlevoix, the Landing is a great spot for lunch/drinks.
Be aware of wind and waves.
You could definitely make a day of it on Walloon Lake, especially if you are planning to jump off the boat for some swimming and get lunch somewhere (or you could do a picnic). Charlevoix is significantly bigger though, and offers more to see. As long as you have a good weather day, you shouldn't need to worry much about wind or waves on either lake, Walloon in particular is generally pretty calm.