Please review this option:
- Define generic hub interface in your Service (or better Domain) Layer project. Something like 
IMessageBroker. 
- Inside your Presentation Layer (WebAPI) project implement this interface and use 
IConnectionManager for HubContext retrieving. 
- Register the interface in an IoC Container (Autofac) in the Presentation Layer
 
- Inject the interface inside App Service
 
Pseudo Code:
Domain Layer:
public interface IMessageBroker
{
    void ShowNewMessage(string message)
}
Service Layer:
public class NotificationService: INotificationService
{
    private readonly IMessageBroker _messageBroker;
    public NotificationService(IMessageBroker messageBroker)
    {
        _messageBroker = messageBroker;
    }
    public void RunNotification(string message)
    {
        _messageBroker.ShowNewMessage(message);
    }
}
Presentation Layer:
[HubName("messages")]
public class MessageHub: Hub
{
    public void ShowNewMessage(string message)
    {
        Clients.All.showMessageOnPage(message);
    }
}
public class MessageBroker: IMessageBroker
{
    private readonly IConnectionManager _connectionManager;
    public MessageBroker(IConnectionManager connectionManager)
    {
        _connectionManager = connectionManager;
    }
    public void ShowNewMessage(string message)
    {
        var hub = _connectionManager.GetHubContext<MessageHub>();
        // Use Hub Context and send message
    }
}
Autofac Registration (Presentation Layer):
// Register Hubs
builder.RegisterHubs(Assembly.GetExecutingAssembly());
// Register Autofac resolver into container to be set into HubConfiguration later
builder.RegisterType<AutofacDependencyResolver>().As<IDependencyResolver>().SingleInstance();
// Register ConnectionManager as IConnectionManager so that you can get hub context via IConnectionManager injected to your service
builder.RegisterType<ConnectionManager>().As<IConnectionManager>().SingleInstance();
// Register interface
builder.RegisterType<MessageBroker>().As<IMessageBroker>();
Also similar SO topic is available here.