We visited Willis Tower with a pre-purchase ticket which was the best option. Wheelchair users do not need to join the general line, go and see a staff member at the front of the line and they will direct you. It is still rather a long time to wait though even from the front door. Once at the top of the tower the views of the city are amazing. We had a great experience and they even allowed me to roll on the glass deck which was a chilling.
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