If it's a product labeled for subcutaneous(under the skin) administration, give it under the skin!
It's always preferable to give an injection subcutaneously, if the label says that's an acceptable route - even if it's also cleared for intramuscular injection.
Dun's right - think about what it would do in a muscle. Get over your aggravation about subcutaneous knots.
Heck, if I were buying calves and saw a knot under the skin up on the neck, I'd be more inclined to think that the producer was actually doing what they're supposed to with regard to vaccinations, and I'd be more inclined to bid on those calves, than ones with no knot.
Beef Quality Assurance(BQA) -
http://www.bqa.org/codeproducts.aspx - we've been working for nearly 30 years to get people to stop giving stuff 'in the muscle' - we're all 'judged' by the consumer by our endproduct - BEEF, and those of us who do it the 'right' way get incriminated and pay the price when somebody sticks a Clostridial vaccine in a muscle and some housewife ends up with a roast or steak with a big encapsulated abscess in it, or the packer has to trim out a big blemish caused by somebody sticking a vaccine in the top of the hip, or injecting 40 cc of LA-200 all in one place.