Is a N2 or CO2 paintball tank a viable power source for a LEGO pneumatic Engine?
Apprently, it is possible to generate up to 37psi with LEGO pneumatics parts only.

LEGO penumatics can withstand more, however. Engines similar to the one you want to build can work with a recommended pressure intake of 90psi; a maximal (but not recommended) of 120psi is mentionned.

So I think it all boils down to the pressure your N2 or CO2 tanks can generate, under 100psi should be OK. If not, I suppose there could be some way to get it down to that level.

As for using N2 or CO2 instead of air, I don't think there is much reason for concern, since both are faily harmless and present in air anyway.