After 4 years of such greetings, I don't think there's much you can do without creating an awkward situation and a certain tension at every future greeting. You can vary the degree of awkwardness and tension, though.
On the other hand, you won't get rid of the discomfort by just letting him kiss you every time. But first thing's first.
Make your husband understand that this is bothering you. If he wants to just brush it off, tell him that it is a big deal for you and that you're planning to do something about it. Don't make him do the work for you, though, but do talk it over with him and tell him what you are planning.
Once you meet with his father, make sure you're out of earshot of others - you don't want to embarrass anyone, right? Then just tell him about it. Tell him you've always felt that way and were afraid to tell him because you didn't want to offend, but you just have to because you're feeling too uncomfortable about him doing it. (I assume this is all true, if not then change it to match your situation.)
Don't tell him what you said in the comment to Martin's answer, that "it's your body to do with as you please". That sounds like an attack and it would put him on the defensive and create further tension. The conversation could go either way - he could be offended, try to make you feel embarrassed, or he could agree not to kiss you any more and laugh about it with you. That really depends on his character and there's really nothing you can do to control his ultimate reaction.
If he agrees not to kiss you any more, the only further thing you need to say on the topic is "thank you". Resist the temptation to elaborate, and change subjects (it might help to pick a subject to talk about beforehand).
In case he is offended say you're sorry to have caused offense, that it wasn't your intention, but you can't help feeling uncomfortable about it every time. Maybe next time avoid greeting him entirely?
In any case, weigh your options carefully.