What can I do about this problem? I need to give my autistic son a flu vaccine.

I am looking for advise on this issue.
My son is now a young adult. He is still seeing his Pediatrician. Last year he gave him flu mist. This year they will not have it. They claim they threw most of it out.
Duane Reade has it but, the Pharmacist are not very supportive. This Pharmacist Mike on Richmond Ave in SI, said I can only do it if, he cooperates. What a clueless jerk.
I guess I have to have the doctor inject him and bring someone from his program to help. FYI insurance and Medicaid will not cover it at the Pharmacy. What should I do? I am very concerned about protecting his health.