One way to start the process of desensitizing your horse to needles is to get your horse very accustomed to having your hands on his neck, occasionally pinching skin between your thumb and pointer finger. Progress to pinching in areas where you will be vaccinating, and harder pinches held for longer periods of time, with smaller amounts of skin. Reward or even distract to start, with sugar cubes, cookies, carrots - whatever works. Next you can progress to using toothpicks to simulate a needle, poking your horse. Do this at random and often times to the point where it becomes a non-event to your horse.
Some other ideas might be: to blindfold the horse (only do this if you are very experienced) - make sure the blindfold may be easily removed or can come off if the horse were to get loose. If you gently pull the horse's nose toward you, you will find the tension in their neck is released a little, in which case they might not react so violently to a needle sliding into muscle on that side. A last tip is to ice the area you intend to prick with the needle; numb the area and the horse might not notice the needle.
Make sure that whatever roundabout ways you might use to vaccinate your horse, that you always have correct technique in applying the needle: the actual application should be quick. Personally, I often stick the needle in the horse's neck then attach the vaccination syringe to the needle. Before you do this, practice removing and re-attaching the syringe to the needle a few times, to get the right feeling. Once the needle is in the neck and the syringe is attached, draw back on the plunger to ensure you have not hit a vein or artery, then assertively (but not too quickly) inject the vaccine. Ensure you know where to place the needle in the horse: the hindquarters are the best muscle to inject because they are large however the neck is usually the safest with most horses. The pectoral muscles, though also appropriate as a vaccination site, can become sore if injected because they are a smaller muscle group. This site clearly outlines appropriate vaccination sites.
For information pertaining to what vaccines are appropriate to your horse in your specific area, consult your veterinarian. You can also ask your vet about performing blood titres to assess immunity and thus the necessity (or lack thereof) for vaccinating your horse.