Lionel uses three types of JST connectors for much of their equipment, the 2.54mm, the 2mm, and the 1.5mm connectors.
JST EH 2.54mm
JST PH 2.0mm
JST ZH 1.5mm
You can find all of them at Digikey. The listings have the mating connectors as well.
For the crimp tool, check out the thread Lionel & MTH Connector Crimper, I already did this research.