If your 3-year-old is anything like mine, the Metro will totally be the highlight of the day. I'd head to American History's America On the Move exhibit, which features really locomotives, cars, and a streetcar that you can sit in with lights and sounds.
Then I'd go outside, maybe ride the carousel, run around on the mall, and eat lunch--either a picnic outside if it's nice, or one of the museum cafes (Natural History's is closed for renovation. American History's is fine for families, but American Indian has great food).
Then, I'd either do the Sesame Street planetarium show that someone else mentioned at Air and Space, OR the Insect Zoo at Natural History, and then go home. He'll probably fall asleep on Metro ride home