They're *completely* different basses.
Having never played a Bongo, I can't really comment on them. I'm not particularly fond of the looks, but then again, I'm not a fan of the looks of the Stingray either, whereas the Sterling is just different enough to be appealing to me, so looks are kind of out the door. I have played a single-pickup Sterling before, and I really liked it . . . not enough to buy it, but enough to change my opinion of Ernie Ball/MusicMan basses. The single-pickup with the coil-tap switch is SUPER-versatile, and very easy to use. I also liked the slim neck and the more contoured, slimmer body, compared to the Stingray.
Once again, having never played a Bongo, I can't really comment at all. Some people here swear by them; others make jokes about their appearance. The only things I have to go on are (a)a clip of Sterling Ball demonstrating the Bongo, in which I thought it sounded like absolute crap (basically, the advertisement backfired on me), and (b)hearing clips of stuff that Tony Levin recorded with his Bongo, which I thought sounded amazing. So yeah, I really have no idea what a Bongo is like in reality.
Paint chipping off necks is uncommon unless the bass is incredibly cheaply-made or if it is severely beaten up and dropped and so on. I'm a fan of painted necks, but honestly, a lot of it is looks. Considering how different the two basses are, I would suggest you try playing both of them and decide which you like more.
Also, bear in mind that there are humbucker, dual-humbucker and humbucker + single-coil options for both the Sterling and the Bongo last I checked, so there's a lot of mixing and matching you can do.