They are not pretty much the same. Not even close.
SH3 lets you run other boats - the Type II, Type IX and Type XXI. SH5 only lets you run the Type VII, but it gives you the Type VII A, B, C and C-41 (I think). It also gives you the full interior of each boat, with some animated crew spread all around.
SH3 gives you a full crew list, but you mostly don't actually see them. SH5 does away with the full crew in favor of a handful you can talk to.
SH3 has a couple of major add-ons that work wonders for the game, such as the Merchant Fleet Mod, which includes more than 70 new merchant types, and SH3 Commander, which gives you a lot of control over your career and (my favorite) adds real historic names to the ships you sink. SH5 is still stuck with around 10 merchant types. Though there are people working on it, they still haven't been able to add more.
The bottom line is that which is "better" really depends on what kind of game you want to play. They are very different, and both have a lot of fans.
On the other hand, they are both cheap enough that you could buy both and try them for yourself.
