¿Eso es con queso? is correct but I think the best way would be to say:
¿Eso tiene queso?
In this case it is best to use the verb "tener".
If you are asking for the content of some food and you want to know if it has cheese then you use tiene (tener)
You would use "ser (es)" if you see something you do not recognize but you think it is cheese. Then you could say:
¿Es eso queso? = Is that cheese?
There is an alternative if what you want to know is if something was made with cheese. Then you do use con
¿Eso está hecho con queso? = Was that made with cheese?
If you are wondering if something comes with cheese on the side then you ask:
¿Eso viene con queso? = Does that come with cheese?
I guess that covers most situations, but in any case if it is/comes/has cheese I'd take it :-)
As fedorqui said in the comments there is also:
¿Eso lleva queso?
This will translate the same as "does that have cheese?". Lleva will also be commonly used when talking about recipes like saying "The recipe asks for cheese"="La receta lleva queso".