If you need to be sure that you're isolating specific enzymes from mitochondria or peroxysomes, I think you need to purify both of your preparations (by gradients) and use antibodies against control markers such as VDAC, citrate synthase, succinate dehydrogenase, etc. for mitochondria and maybe catalase, urate oxidase, and DHAP acyltransferase for peroxysomes. You can also determine organelle-specific enzyme activities from each fraction. Second, mitochondria usually could be mostly separated at 10,000 rpm (10-15 min) and peroxysomes at 40,000 rpm (1 h). Once your fraction is pure (by gradients), enzyme isolation can be performed using detergents such as Triton X-100, laurylmaltoside, digitonin, native- or denaturant-PAGE, classical cromatography columns and others.