One option that you have is to create two separate views—one for iOS with a search box in the header and one for Android with a search box in the footer. Then, you can use the Device core plugin to check which is the current OS and open the respective view for filtering.
I have implemented such approach in the attached sample. When you open the drawer and click Search, based on the device platform, a different version of the view is opened. This happens in the click event handler of the link that I have attached during deviceready in app.js:
platform = device.platform.toLowerCase();