[OT] Jupiter

Calling some vacc-head astrophysics/planetologist types:

I just checked out some Jupiter data (need some gas giant info for FT
scenario). It looks like 140K km diameter. Now, is this with atmosphere?
If not, how large would the diameter of the atmosphere be (from the
point where it would likely be dense enough to be noticeable to a
starship)? 

I'm just happy with some ballpark guesses. No need for Physics 404. ;) 

PS - What effects do we suspect in-atmosphere ops might have? (ie
shields don't work, sensors don't work well, firing impeded, etc, heavy
gravity, etc)