Querying an array of users
Thanks to Jason and Ben for the assist. I changed tac a bit and moved the field on to the user (as an Entries field). Now got this working:

{# Display unread notifications for current user #}
{% set notificationsRead = currentUser.userNotificationsRead.ids() %}
{% set notifications = craft.entries
    .id(['not']|merge(notificationsRead))
    .section('notifications')
    .all() %}

{% for entry in notifications %}
    {{ entry.title }}
{% endfor %}