We just did a similar trip last year with a 3 year old and less than one year old and had a blast.

The kids loved Alligator World (which has much than just alligators), Sawgrass Lake Park in St. Petersburg (public park w/ wild alligators, turtles, and frogs you can see on a nice trail), Anne's Beach in the keys (very calm water, kids loved the hermit crabs), Cape Canaveral (we were able to watch a rocket launch while we were there), a helicopter flight in Orlando (only $63 for all 4 of us), Fort DeSoto State Park (watching dolphins from the pier and great sand for playing in), South Florida Museum (has a great planetarium show and Snooty the manatee) and just hanging out at the Sheraton Vistana Villages pool and enjoying the resort activities.

Things we tried to do that we wouldn't do again were Clearwater Beach, which just didn't have much for our age of kids (probably better for older kids), airboat tour (too loud for the kids). I wish we'd had time to do the Tampa Zoo and the Miami Seaquarium.