You could exploit Laravel collections to achieve what you need.

Most of your code is checking for the presence/absence of props on your arrays. Laravel internally exposes and uses the Illuminate\Support\Arr class that contains a lot of useful methods to work with arrays without the hassles of checking for key existance.
It also allows you to use dot notation to get nested properties in a really simple way.

Laravel collection methods (documentation) uses this class where needed. Therefore, the refactored code would become really intuitive and should look like this (it may need a little bit of tweaking based on your userNotificationPreference and preferences arrays and how you retrieve them from the model:

$recipients->map->getUser()
    ->where("userNotificationPreference.preferences.{$sendMethod}", true)
    ->where("userNotificationPreference.preferences.specific-templates.0.{$notification->getTemplateCode()}.0.{$sendMethod}", true);

Note that I used ->map->getUser() that would be equivalent to:

$recipients->map(function ($recipient) {
    return $recipient->getUser();
})

However, if you really need to pluck the user instance through the user repository then you can do:

$recipients->map(function ($recipient) use ($userRepository) {
    return $userRepository->findByParams([
        'email' => $recipient->getUser()->email
    ]);
})->where(...);

and chain the where calls after that.

If any part of my code is unclear or doesn't work, let me know in the comments and I'll explain/fix it.

You could exploit Laravel collections to achieve what you need.

Most of your code is checking for the presence/absence of props on your arrays. Laravel internally exposes and uses the Illuminate\Support\Arr class that contains a lot of useful methods to work with arrays without the hassles of checking for key existance.
It also allows you to use dot notation to get nested properties in a really simple way.

Laravel collection methods (documentation) use this class where needed. Therefore, the refactored code would become really intuitive and should look like this (it may need a little bit of tweaking based on your userNotificationPreference and preferences arrays and how you retrieve them from the model:

$recipients->map->getUser()
    ->where("userNotificationPreference.preferences.{$sendMethod}", true)
    ->where("userNotificationPreference.preferences.specific-templates.0.{$notification->getTemplateCode()}.0.{$sendMethod}", true);

Note that I used ->map->getUser() that would be equivalent to:

$recipients->map(function ($recipient) {
    return $recipient->getUser();
})

However, if you really need to pluck the user instance through the user repository then you can do:

$recipients->map(function ($recipient) use ($userRepository) {
    return $userRepository->findByParams([
        'email' => $recipient->getUser()->email
    ]);
})->where(...);

and chain the where calls after that.

If any part of my code is unclear or doesn't work, let me know in the comments and I'll explain/fix it.