A couple of ways;
Use remote i/o modules and connect to your PLC using screened cable and lightning arrestors.
Run each line in screened cable and fit a lightning suppressor to each line. Pheonix contact Trabtech for instance. However I would not reccommend using 24v dc signals with 1000ft of cable.
The best way would be to use a small PLC nearby to collect the inputs and connect to the main system with a field bus system such as devicenet. If interference is a big problem then perhaps consider fibre-optics.