Unit testing a generic query factory

I have implemented a command/query architecture for a project I am working on, but am having trouble testing my classes that require use of the associated factories. The basis of my architecture can be found here: http://ift.tt/XWiswO

In particular, I have something similar to the following

public interface IQueryFactory
{
    TQuery CreateQuery<TQuery, TResult>() 
        where TQuery : IQuery<TResult>;
}

public interface IQuery<TResult>
{
} 

public interface IQueryHandler<in TQuery, out TResult>
    where TQuery : IQuery<TResult>
{
    TResult Execute(TQuery query);
}

public interface IQueryHandlerFactory
{
    IQueryHandler<TQuery, TResult> CreateQueryHandler<TQuery, TResult>()
        where TQuery : IQuery<TResult>;
}

public class GetFooDataQuery : IQuery<IEnumerable<FooData>>
{   
    public int FooId { get; set; }
}

public class GetFooQueryHandler : IQueryHandler<GetFooDataQuery, IEnumerable<FooData>>
{        
    private readonly IFooRepository _fooRepository;

    public GetFooDataQueryHandler(IFooRepository fooRepository)
    {          
        _fooRepository = fooRepository;
    }

    public IEnumerable<FooData> Execute(GetFooDataQuery query)
    {           
        return    _fooRepository.Foo.Where(x => x.fooId > query.FooId).ToList();            
    }
}

My classes that need to query the database have a constructor that includes a query factory and a query handler factory. Everything gets wired up via Ninject.

It works fine, but I am finding it difficult to create Unit tests for any class that includes query factories as I need to include the factories as part of the constructor. Any help would be greatly appreciated.