The IX subs are bigger, faster, go further and carry more eels and more flak early on but they're slower to dive, less maneuvarable when submerged, and larger so far easier to find by active sonar.
It's a tradeoff, for long patrols to exotic places, take the IX, you can still take on convoys and yes, even harbor raid with it but it's trickier
for your basic "battle of the atlantic" or for you rabid raiders out there, I'd say the VIIc
I personally like the IXb best, not too big, still goes a long way and has a lot of eels
