How to implement generic GetById() where Id can be of various types

You should remove the constraint on TId from your Repository class

public abstract class Repository<TEntity, TId> : IRepository<TEntity, TId>
where TEntity : class, IEntity<TId>
{
    public virtual TEntity GetById(TId id)
    {
        return context.Set<TEntity>().Find(id);
    }
}

To your question:
I am trying to implement a generic GetById(T id) method which will cater for types which may have differing ID types. In my example, I have an entity which has an ID of type int, and one of type string.

    public virtual TEntity GetById<TId>(TId id)
    {
        return context.Set<TEntity>().SingleOrDefault(x => x.Id == id);
    }

For generic parameter, just make a generic method like above

public interface IEntity<TId> where TId : class
{
    TId Id { get; set; }
}

The where TId : class constraint requires every implementation to have a Id which derives from object which is not true for value types like int.

Thats what the error message tells you: The type 'int' must be a reference type in order to use it as parameter 'TId' in the generic type of method IEntity

Just remove the constraint where TId : class from IEntity<TId>