Well - it used to be a little known fact (mebbe you can change it to say the continental 48 states). Google it - I'm sure the real answers are out there.
I went up to google and found that Anchorage, Alaska covers something like 1,756 sq. miles, where Jax is 759, if I remember correctly from yesterdays search. The only reason I knew that JAX was no longer the largest of all fifty states is that it cost me fifty bucks back in the mid eighties. As far as the 48 contiguous states, JAX's has held the record for quite some time.
Georgia, which I believe has the most counties of any state, could save a ton of tax money by reducing the number of counties. Of course the county politicians would never let that see the light of day. As far as people saying that Savannah, Georgia is so much greater than JAX or SC, after living in Savannah for over seven years, I wouldn't brag that much about that place. The Schools are terrible and most people in SAV are drop outs. Other than the great Deep Sea Fishing, Seafood, and pristine unpopulated coastline. Georgia is mixture of two states within the state. The Metro Atlanta area is completely different from the rest of the state as far as the people go.
From Wikipedia: Sitka, AK
According to the United States Census Bureau, the borough is the largest incorporated area in the U.S, with a total area of 12,461.8 km² (4,811.5 mi²). 7,443.6 km² (2,874.0 mi²) of it is land and 5,018.2 km² (1,937.6 mi²) of it, or 40.27%, is water.
Sitka displaced Juneau, Alaska as the largest city upon the 2000 incorporation with 2,874 square miles of incorporated area. Juneau is 2,717 square miles and was formed through incorporation of the borough and city in 1970. Jacksonville, Florida is the largest city in area in the contiguous 48 states at 758 square miles.