The only tool I use is an ST-303 e-unit spreader. It has a cam to pop apart the e-unit without having the pieces fly all over. You can purchase a reproduction one from just about any Lionel parts dealer. They are inexpensive.
Some folks like to use something like a proto lock ring plier (model 250G) to spread the sides.
I have a number of other e-unit tools, including those pliers, e-unit vise, and some other third party tools. As I wrote above, the spreader is the only one I use. Currently the Train Tender gets $3.50 for them.