You could use a specific antibody that is expressed on the exosomes and separate using facs sorter or antibody -bead separation to separate cell specific exosomes . I think if you want a complete exosomes Ultracentrifuge is the best way.

Hi there! If you are trying to visualize the mitochondria, how about isolating your mitochondria in a suspension of PBS (or whatever buffer you might use), then fixing them in 3% glutaraldehyde in buffer? You could then centrifuge, pour off the fix and re-suspend in a PBS rinse. Take a drop of the suspension and apply it to a formvar/carbon coated grid, let it dry and examine on a TEM. You might get further enhancement with a uranyl acetate negative stain. Shadow-casting would be recommended but not absolutely necessary. I just don't know how beat up your mitochondria would be, but I have done exosomal suspensions before with good results. It's all in the sample prep. Good luck! I can give you more details if this idea appeals to you.

I have successfully used the protocol in available via Cerrent Protocols to itsy isolate exosomes from conditioned culture medium.  It is a long process, but effective.

http://onlinelibrary.wiley.com/doi/10.1002/0471143030.cb0322s30/abstract

Centrifugate at 2000g for 20 min, recover the supernatant

Centrifugate 2x at 12000g for 45 min, recover the supernatant

Filter through a 200nm pore filter to remove bigger vesicles

Centrifuge at 110.000g for 2h, discard supernatant and wash pellet with PBS

Centrifuge at 110.000g for 2h and remove all PBS, the pellet (you won't see anything) are your exosomes

we used this protocol, and the result seems better  than kits.

Article Isolation and characterization of exosomes from cell culture...