Here’s the thing that I keep seeing. Unless you have an abnormally large number of page views, advertising is probably not going to be a big source of income for you. You might get work from the website, be that consulting or illustrating, though that may take years to see that happen. If the NY Times has its way, people will get accustomed to paying subscriptions and micropayments but I wouldn’t suggest holding your breath on that.
-Robert H. Schuller
So if you have a website and you want to make money from it, then have something to sell. Perhaps it is your comic, perhaps it is closely related merch that your audience will enjoy. I’ve never had much success with affiliate programs like Amazon or Commission Junction but some report success.
Perhaps you could convert parts of your website into an ebook? It seems like it would be worth trying out, whether that is generating a comic pdf from your latest comic updates or making a best-of comic ebook. There are lots of potential products, depending on your comic and audience.