-Six Flags Great Adventure (about an hour and a half from New York City in Jackson, NJ)
-Kings Dominion (about an hour and a half from Washington D.C. in Doswell, VA)
-Six Flags Great America (about an hour from Chicago in Gurnee, IL)
If you're up for a bit more driving (up to three hours each direction), you could also go for:
-Six Flags New England in Agawam, MA
-Hersheypark in Hershey, PA
-Busch Gardens Williamsburg in Williamsburg, VA
Finally, if you are driving between destinations, you may want to look into Cedar Point (Sandusky, OH), although this will require two of your three park days.
I've been to most of the parks listed above (never been to Hersheypark or Six Flags Great America) and assuming you're only interested in roller coasters I'd recommend you definitely do Six Flags Great Adventure. If you can, try to do Cedar Point. If you can't do Cedar Point, do Kings Dominion and either Six Flags New England or Six Flags Great America. In the event that you are driving from New York to Washington D.C., you could do Hersheypark instead of one of these, but this would require spending a night near the park. Finally, you could substitute Busch Gardens Williamsburg for Kings Dominion (or do both if you don't mind staying in Virginia overnight), but Busch Gardens only has five adult coasters (they are five good coasters, so it's a quantity vs quality thing) while Kings Dominion has 12 (plus two kiddies).
Anyway, SFGA and SFGAdv are probably two of the top parks in the SF chain. SFGAdv has a zoo connected to it and much more of a resort. SFGA is pretty much a nice theme park, thats it. However, their collection of roller coasters are diverse and plenty
And I wouldn't call the Safari a "Zoo." That word implies patrons walking around and looking at animals in cages or fenced-off habitats. The drive-through-yourself Safari is about to end permanently, if it hasn't already. Beginning next season, you'll be able to ride in a military-type multi-passenger vehicle and see the animals up close. That will be included with park admission, unlike recent years. Now, Hershey's ZooAmerica...THAT's a zoo!