Hello Daniella!!!!
WOO HOO!!!! It's your first time to Disney World, and you are going to experience the Disney Magic with two incredible kids!! You really are going to have the best time!
I would have to say the best Disney Theme Parks to visit with a three and six year old are Magic Kingdom and Hollywood Studios!
Magic Kingdom: All the attractions and rides are based on movies and Disney characters they will recognize. When you arrive at Magic Kingdom, go straight to Fantasyland. Every attraction in this area is built for families with small children. There are definitely other great things to do with your family in Magic Kingdom!!! Click
HERE for a complete list of all the Magic Kingdom attractions.
Hollywood Studios: If your children love Disney/Pixar characters, then they will LOVE Hollywood Studios. Disney has just launched a brand new parade featuring all of your favorite Disney/Pixar characters including Monsters, Inc. and Toy Story. And speaking of Toy Story, don't forget to ride the most incredible attraction at Hollywood Studios, Toy Story Mania!! They will also love Beauty and the Beast -Live on Stage as well as the Voyage of the Little Mermaid stage show. My kids also love the "Honey, I Shrunk the Kids" Movie Set Adventure Playground! For a complete list of Hollywood Studios attractions, click
HERE.
I hope this helps in your planning! If you have other questions, please let me know!
Have a MAGICAL day!