Aquarium & Reef Center off Del Prado just celebrated 18 years in business on Saturday so they've outlasted quite a few others. Brandi and John there are great. They don't always have a ton of fish, but they also don't turn and burn fish and coral. If something doesn't look healthy or isn't eating, they won't sell it to you. They also have a sister store in Fort Myers which is a bit larger worth checking out. Boardroom Aquariums is a few blocks away from the Fort Myers location so you can hit both at the same time.
Seven Seas in Cape Coral is newer and usually has all the major brands of equipment in stock. They just expanded their fish holding tanks but have tons of coral tanks as well.