[enaceo]

When it comes to upgrading to the IX (if that's what you're talking about) you should wait a bit untill the IX/C(or the IX/D2 if you don't mind the range bug and the fact that it comes out a bit later in the war)comes out and not get the IXB right away.The VIIC isn't that bad and can be used untill the later IX versions or if you want the XXI come available.
Which sub is the best?Well,hard to really say...the IIA-IID are best for the early-war period,for attacking ports without being detected...but they get kind of obsolete with time...the VIIB/C/C40 whatever is a very balanced sub .Good range -but you might find that it has too few torps sometimes.
The IX class subs are a bit bigger than the VII's ,have more mass and are a bit slower ,but they have greater range +a lot more torpedoes(I personally like these best).
The XXI is a "special" type of sub.Has some bugs here and there (like the battery bug -but that has a fix for it,or some parts don't function properly) +it is HUGE but has a sh**load of torpedoes in internal rezerves but the problem is it only has frontal torpedoes.Well,we can overlook that ,but sometimes you really need those...Choosing the best sub is really up to you.