Both Nessus and Nikto will only find simple and easily found known bugs. If you build something yourself it's quite likely they won't find any problems even if it's written completely insecure.
While they are good for a quick scan don't rely on them too much. If both applications can't find anything it could still mean your web application has bugs.
I am co-founder of Orvant. We have a product which allows you to OpenVas, Nikto and W3aF (both external and internal) through our portal. W3af is going to be the best bet of those three as it's not just working of a database of know threats but actually tries to determine the the inputs on the page runs different attack vectors on them. We also support some non-open commercial tools which may be usefull. You can check us out at http://www.orvant.com
Having said that, if you're a developer you still should follow the recommendations found here:
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