Preschoolers are a good age for a wide range of exhibits at MSI.
Idea Factory on the lower level is a fun, interactive space for preschoolers with lots of balls, water, blocks, and other things to play with. You'll need a free timed ticket to go in, you can get those by the entrance (you can choose any time that day, but there's a cap for each time slot so the tickets for immediate entry are often gone, you'll likely need to wait 10-60 minutes depending on how busy the day is). Although there are a few ways to play with water, most kids will stay dry if you roll up sleeves—still, it never hurts to have a backup set of clothes available.
Farm Tech is next to Idea Factory (and I'd recommend grabbing the timed tickets for Idea Factory, then playing in Farm Tech until they're ready). The highlights are a real tractor and combine that kids love to climb in and play with. If the line for one is long, try the other, they're often very uneven. Around the corner from the tractor are a couple of pretend cows to milk.
Flight on the top floor is a real Boeing 727 that kids will love to play in (and was helpful to explore and make my kids comfortable before their first flight). The video playing just outside the plane has the very interesting story of the Boeing 727 in general, and of how they got this one to the museum.
The U-505 is a real captured German submarine and a fantastic exhibit for this age. With preschoolers who might not be interested in war or comfortable talking about ships sinking, I often walk through the lead up to the submarine without stopping to look at the exhibits. If you want to skip it completely, see the U-505 page for information about how to do that. I strongly recommend against the on-board tour for kids this age.
The Great Train Story with its giant set of model trains and transportation gallery in general are a big hit for preschoolers. Next door, Genetics has baby chicks that are fun to watch.
The Henry Crown Space Center is enjoyable for preschoolers, with a real Apollo capsule and a practice lunar lander on display, along with a few fun interactive exhibits.
Science Storms will be interesting to preschoolers (especially the giant "tornado") although most of the explanation in content will be at a level too advanced for them.
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