There are three main resorts (hotels) that I would stay at. Please understand that I am a local and have not stayed at any of these but give you a perspective of the resort from a local.
Hyatt Clearwater Beach - An excellent family resort, located directly in the middle of Clearwater Beach. Has a pool, shops, restaurants, parking garage, and overlooks the beach! Excellent access to all local attractions.
Sandpearl Resort - A very high end resort located at the northern end of Clearwater Beach. Not as much attractions nearby, but within a good walking distance. (There are public buses that can take you down the beach for a small charge). This resort is actually on the beach, a huge plus.
Sheraton Sand Key - A beautiful resort that is located just south of Clearwater Beach. Again, the public buses can take you to the main beach area for attractions. Located in Sand Key, they have a private beach but not as award winning as Clearwater Beach. Very peaceful and not as busy as Clearwater though.
Shephards Beach Resort - Would not recommend this for a family, this is more for young couples and singles that want a party atmosphere. They have alot of live music and night clubs. The breakfast buffet is worth coming too even if you do not stay here.
Hope this helps. There are plenty of attractions at the beach to keep you busy besides the beach itself.
Regards,
Joe
References:
Clearwater-beach-vacation.com