How much vinegar should I use when making Salsa?
The guideline for the safe canning of tomatoes is for 2 tbsp of 5% vinegar per pint of tomatoes. If you made 16 pints then you'd need 32 tbsp of vinegar, and that is almost 2.5 cups. This isn't to prevent spoiling, the processing will do that, it's to prevent the growth of botulism, which boiling does not do. 

However, the recipe above calls for 16 cups of tomatoes, 4 cups of onions and 2 cups of jalapenos, for a total of 22 cups of vegetables. That's 11 pints, not 16, so if you added 2.5 cups to that you've gone almost 50% over the amount you need, which could account for the strong acid flavor. For that volume 22 tbsp or 1.65 cups would be sufficient. 

It's possible your wife's boss is adding vinegar until it tastes good, then canning the result. This isn't safe because it means there could be far less acidity than would be wise (I'm assuming that the boss is using a water bath method because that's what the recipe says, if she's using a pressure canner then it's a different story). If this is the case then this recipe will never really work as is because to make it taste right you'll have to compromise on food safety. 

You have a couple of options here: 


Buy a pressure canner: you can probably ebay one for not much money, and it means you can get the flavor you want. Processing time is much shorter as well, giving you superior product (the guidelines for a water bath are 40-50 minutes, in a pressure canner it's just over 10)
Try a different acid: citric acid powder adds acidity without much flavor. The guideline is 1/4 tsp per pint. Canning supply shops will carry it, it's easy to find on the internet. Lemon juice (commercially bottled for consistency) is also a favorite for salsas, 1 tbsp per pint is the guideline. 


If you decide to change acids or acid levels then I suggest you do a small test batch to make sure it's good before going full scale. 

A good page on canning tomato products is here.