Angie,
The dock where the boat unloads at Downtown Disney (Cap'n Jack's Marina) is actually at the extreme east end of the Marketplace, so you are looking at a good 10-15 minute walk from the dock to where
DisneyQuest and the
Wolfgang Puck Cafe are located.
Wolfgang Puck Express is closer to the dock, really just a quick 2-3 minute walk.
If you really would like to visualize it, I recommend visiting the website
www.WillCAD.org and looking at a map of the place. This unofficial site has scanned maps of Disney resorts and parks, as well as Downtown Disney, and they can help you visualize your walking time.
As to it being too far to walk with two kids, no, I don't think so. There is a lot going on, so plenty of distractions during the walk. When I do it with my two kids (both under 4 years old), I certainly have my stroller with me, but it is not a hardship, by any means.
I hope that this helps?
Have a magical vacation!