I remember that episode. It actually was the one, that started off a bunch of versions on the same theme.
Like there's a Rugrats episode, where Chuckie swallows a watermelon seed. So the babies shrink down and go inside Chuckie, to get the seed so it won't grow inside him. However Angelica has other plans, and she waters the seed to make it grow. Then Chuckie wakes up and realizes it was all a nightmare. Then Spike swallows the seed, and they show the kids about to shrink again, as Angelica says "Has anyone ever been in a dog before?"
There's a Magic School Bus game for PC, called Magic Schoolbus Inside the Body, or something similar to that. It really isn't all that interactive, as much as it's meant to drill educational facts into your brain. They do have some cool 3-D cutscenes where the ship travels into different parts of the body. Also if you click on the kid with the green shirt, in the back of the bus..you can play mini-games on his portable video game system.