As a webmaster, I'd rather they email me directly rather than the owner of the site, since I'm going to see it eventually anyway and I'm in charge of the linking campaign. I wouldn't put my email there if I didn't want to be contacted about the website.
generally if there is not a form on the site or a specific contact email address given - then your chances of getting a link are low, of course there are exceptions to this, it will depend on how much time you want to spend trying to get links.
If you are going to ask a company/site about something then it is pointless guessing the email so unless the site clearly states who you should email for a specific type of query then the best thing to do is alwys to email the site and ask who you should contact explaining that you are interested in obtaining a link on the site.
They will then have more chance of replying than if you sent a load of detail to someone who is potentially not interested in/able to deal with your query.
The best way to approch things is to get your foot in the door first don't even ask about links just ask who it is that deals with updating the website content a short direct question will normally get a response other emails are much more likely to be trashed.