We're following Dad on a short business trip with our son. What's the best destination with a four yr old?

We've never gone wrong with either the museum of natural history (especially all the dinosaurs) or the air and space museum. Even a 4 year old will get something out of both of those!

The Smithsonian's Postal Museum (next to Union Station) was a huge hit with my four-year old nephew, largely because it was all about moving the mail and little boys are usually crazy about transportation -- trains, pony express wagon, small airplane, trucks, etc. He also enjoyed using various means of transportation to get around, especially riding Metro backwards toward National Airport.
(Of course, if you are coming from NYC, the subway would not be the adventure it was for a little boy from Kentucky.)

Visit the Old Postal Pavilion (Federal Triangle metro), and take the free tour up to the top of the clock tower & look out. Small food court in the basement for some refreshments too.

Would a 4 y/o be too young to take on a paddleboat (human powered) ride? Located in Basin near Roul Wallemberg (sp?).

My kids enjoyed the DC Ducks. It was a fun way to see the sights and get an overview of the city. After taking you by the museums and monuments, the amphibious vehicles plunge into the Potomac river for a ride near the Jefferson Mem'l, the Reagan National airport and then back on land and back to Union Station. Our kids even got to drive the "duck". 90 minutes of fun on a nice day! I think a four year old would enjoy that.

National Zoo is another good choice