You can implement both. AppIndexing also now affects personalized search ranking , so it may yield better results for your Android users .
Quoted from page above in case the link rots:
Starting today, we will begin to use information from indexed apps as
a factor in ranking for signed-in users who have the app installed. As
a result, we may now surface content from indexed apps more
prominently in search.
If you have a lot of audience on Android, I'd recommend using AppIndexing. If you have a lot of users on Facebook, I'd recommend using App Links. If you have both, do both!
To directly answer your question, you can't rely on App Links to fulfill AppIndexing, but you can probably do the work at the same time with minimal additional effort.
Edit
To better answer your question, you should be able to structure the expected URIs to be the same for both. This would enable the handling of the Intent in the Android client to support both incoming AppLink URIs and AppIndexing URIs.
Edit 2
Example URI structure to support both AppIndexing and AppLinks.
Let's say you have an Android app called SuperLinks with the package name com.example.superlinks, you want to create a schema to address a specific resource, called examplelink #1234. Your URI schema would be superlinks://examplelink/1234 which you could implement the Android client handling once, while adding the 2 differing pieces to the webpage's head.
Your AndroidManifest.xml would contain Intent filters to handle the schema you've created as such (Reference):
...
<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 the action and category flags are necessary for the app to be listed as an option in the chooser when a user attempts to open one of your schema links.
To support AppIndexing, you'd add the following to your page's head (Reference):
<head>
...
<link rel="alternate" href="android-app://com.example.superlinks/superlinks/examplelink/1234" />
...
</head>
To support AppLinks, you'd add the following to your page's head Reference:
<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>
