Comment: Highly recommend USS Cobia tour in Manitowoc, WI (Score 4, Informative) 222
I've been on a lot of tours of WWII vessels-- everything from the USS Arizona in Hawaii to the USS North Carolina in North Carolina to the submarine exhibit at the Deutsches Museum in Munich, Germany.
I have to say the very best tour I've done was the USS Cobia sub tour in Manitowoc, WI. http://www.wisconsinmaritime.org/
The tour was given by an old WWII submariner (yes, he was old!). It was a far better experience than any other sub exhibit. The sub is in the water and it is quite the feeling to go beneath the water line of a WWII sub.
If you are ever in the area, I highly recommend it! Granted that was 12 years ago and nowadays the old tour guides may have either passed or are too feeble...