Having just visited the Lake Superior Railroad Museum last month I can say that it was fantastic! I haven't visited all of the others, but the experience at the LSRM was the best I've ever had. That includes the train ride. I love how they use technology to make the ride and exhibits interactive. I can't wait to go back.
We have been to the ISRM as well and while they may have more equipment, the experience wasn't anywhere near what the LSRM provides. I like both for different reasons. If you prefer a professional museum experience over a collection of trains then I highly recommend the LSRM.
