You can get a relatively inexpensive microscope and telescope at most toy stores, and he's not too young to learn how to use them. A prism is also a great toy. XUMP.com is a great place to find science toys online, and you can search by age. (If you're brave enough, get him an ant farm!)
For home-made items, you can't beat water bottle rockets and water scopes, especially in the summer. To make a water scope, all you have to do is cut off both ends of a large coffe can or large plastic tube and cover one end really tightly with plastic wrap (use a large rubber band, like the kind that comes around veges to secure the wrap). This is great for exploring creeks and ponds -- instant underwater magnification!
Building water rockets is a little more complicated. I found some sites on the web, but everything was a lot more complicated than anything I ever did with my kids. Take a 2-liter bottle and buy a cork to fit the top of the bottle very snuggly. Push a ball valve needle (for blowing up playground balls) through the cork; make sure the needle goes all the way through so that the air hole will be in the bottle when the cork is in place. Build a small 3 or 4 legged stand with a hole in the middle that is small enough that the bottle can nest upside down in it securely, but not so that it's wedged in (your son can have some fun with hammer and nails, too, under your supervision). Fill the bottle about 1/3 to 1/2 full with water (you and your son can experiment with how much water works best). Place the cork tightly in the top of the bottle. Hold your finger over the end of the valve and turn the cork side down in the frame. Quickly attach a bicycle pump to the valve (a foot pump works well) and start pumping! Make sure that no one is leaning over the bottle. When the pressure gets high enough, the cork will pop and the bottle will go flying and spray everyone with water as it goes -- definintely NOT and indoor activity! :-) We've gotten bottle to fly over 50 feet.
Also, a small safety thermometer, funnels, a scale, measuring spoons and cups, a balance scale and almost anything you have around the house can be turned used for a science project. Want to build a Bernoulli blower? All you need is a blow drier, a soccer cone (open at both ends) and a beach ball. I would go looking for a good book on science experiments for preschoolers at the library or book store. Take your son to the CA Science Center and the Kidspace museum in Pasadena for hands-on fun and ideas. Visit the aquarium and the zoo. (I would wait to go to Griffith Observatory for a few years).
Most importantly, encourage your son to constantly ask questions and try to find a way to answer them for himself (at his level of understanding, of course). Why does this happen when I do X? What happens if I do Y instead -- how does that change it? When will A happen if I do B? What can I do to make something work better? First and foremost, have fun!