these two companies are both OK, after all they are the leaders in this industry.
The problem is what kind of technology you want, FDM or SLA(they may don't call their technology as this name).
As I know, it is meaningless if you buy their FDM system, because it is very expensive(not cube or makerbot), I mean their industrial FDM printer, like Mojo.
If SLA technology, 3D system has richer product lines than Stratasys.