You can implement both. AppIndexing now affects personalized search rankings , so it can give better results for your Android users.
Quote from the page above in case the link rots:
Starting today, we will begin to use information from indexed applications as a rating factor for registered users who have the application installed. In As a result, we can now add content from indexed applications more noticeably in the search.
If you have a large audience on Android, I would recommend using AppIndexing. If you have many Facebook users, I would recommend using apps. If you have both, do both!
To answer your question, you cannot rely on App Links to do AppIndexing, but you can probably work at the same time with minimal extra effort.
Edit
To better answer your question, you should be able to structure the expected URIs equally for both. This would allow Intent to be processed in the Android client to support both inbound and URIs of AppIndexing applications.
Edit 2
An example URI structure for supporting AppIndexing and AppLinks applications.
Say you have an Android application called SuperLinks with the package name com.example.superlinks, you want to create a scheme to access a specific resource called examplelink # 1234. Your URI scheme will be superlink: // examplelink / 1234, which you could implement the Android client interface once by adding 2 different fragments to the head of the web page.
Your AndroidManifest.xml will contain Intent filters for processing the scheme you created as such ( Help ): ... <activity android:name=".YourActivity" android:label="@string/app_name" > ... <intent-filter> <action android:name="android.intent.action.VIEW" /> <category android:name="android.intent.category.DEFAULT" /> <data android:scheme="superlinks" /> </intent-filter> </activity> ... Note that action flags and categories are necessary for the application to appear as an option in the selection when the user tries to open one of your schema links.
To support AppIndexing, add the following to your page title ( Help ): <head> ... <link rel="alternate" href="android-app://com.example.superlinks/superlinks/examplelink/1234" /> ... </head>
To support AppLinks, you must add the following to your page Link : <head> ... <meta property="al:android:url" content="superlinks://examplelink/1234"> <meta property="al:android:package" content="com.example.superlinks"> <meta property="al:android:app_name" content="SuperLinks"> ... </head>