I've read up a little bit about the Navionics chips and stuff but I'm still wondering how are they able to map a lake with such accuracy?

Like this, only on a much larger scale, and using accurate GPS and measuring equipment: http://www.bassresource.com/fish_biology/mapping-a-lake.html

Thats pretty cool! But how exactly would they get the data from each body of water? Do they go to each lake in the U.S. and sweep it with sonar?

They'd have to. Remember, this information is important to many outside of fishing - geologists, biologists, Corp of Engineers, Military, etc.

Most man made lakes are mapped before they are flooded. Aerial photogrametry is used to map the topography. This what I do for a living. Licensed land surveyor providing ground control for the photographs.

Ronnie

So for southern reservoirs they survey the land before its flooded, but for natural lakes would they map the entire lake using sonar?

There's no other way, that I know of. Additionally, the lakes bottom changes as time wears on, so older maps may not be as reliable.