If you have to do it in Nebraska then you will be fine taking it across the border into Iowa. We acknowledge all other states boat registration. So as long as you register it in your own state then you'll be fine.
Some states don't require you to get one, then you would need to get an iowa registration which is like $10 for 3 years. Also if your state doesn't require one then you may be able to register it for free anyway (from your home state) - this also helps for insurance matters if anything happens to your boat.