The particle "ni" is used for the location where you enter, thus, "Heya ni haitte mo ii desu ka?" is the answer. "Heya wa haitte mo ii desu ka?" is not incorrect, but it doesn't just mean "May I enter the room?" It's used in a situation, for instance, you are not allowed to enter the garden, and ask "How about the room?". (This "wa" is often called "contrastive marker".)