Best disinfectant for endoscopes is:
Activated 2% alkaline glutaraldehyde is used for decontaminating flexible endoscopes.
Advantages

 Relatively non-corrosive
 Will kill spores with prolonged exposure (3- 10 hours). 

Disadvantages
Toxic. Irritant. 
Possible alternatives:

 Ortho-phthalaldehyde (OPA) peracetic acid.
 Chlorine dioxide (ClO2) products (such as Tristel).
 Super-oxidized water (Sterilox).

Advantages of these newer agents are - rapidly sporicidal, mycobactericidal and viricidal. BUT remember - No agent is clearly superior to the others and a thorough assessment needs to be performed before an alternative agent is chosen.
Hypochlorite
Formaldehyde
Glutaraldehyde
Chlorhexidine